Can't init servlet error after upgrading from 4.2.4 to 5.0.6

I am trying to upgrade my installation of youtrack to 5.0.6, but I am running into trouble. I see the following exception in the errors.log file and the web app is unavailable. Luckily, I was able to revert back to the old version and get the server started again.

Any idea what I can do to get past the exception and get my instance upgraded?

04 Jan 2014 20:13:43,340 ERROR [ServletImpl         ] [init servlet        ] [] Can't init servlet
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transientEntityStore' defined in file [/home/svc-utrack/.youtrack/work/jetty-0.0.0.0-8282-youtrack-5.0.6.jar--any-/webapp/WEB-INF/classes/jetbrains/charisma/persistent/storeConfigurationDatabase.xml]: Cannot resolve reference to bean 'persistentEntityStore' while setting bean property 'persistentStore'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'persistentEntityStore' defined in file [/home/svc-utrack/.youtrack/work/jetty-0.0.0.0-8282-youtrack-5.0.6.jar--any-/webapp/WEB-INF/classes/jetbrains/charisma/persistent/storeConfigurationDatabase.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [jetbrains.exodus.database.PersistentEntityStoreImpl]: Constructor threw exception; nested exception is java.lang.ArrayIndexOutOfBoundsException: 30720
        at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:275)
        at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:104)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1245)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1010)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:472)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory$1.run(AbstractAutowireCapableBeanFactory.java:409)
        at java.security.AccessController.doPrivileged(Native Method)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:380)
        at org.springframework.beans.factory.support.AbstractBeanFactory$2.getObject(AbstractBeanFactory.java:302)
        at webr.framework.controller.WebLocalScope.get(WebLocalScope.java:33)
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:298)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:185)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:164)
        at org.springframework.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:880)
        at webr.framework.controller.WebLocalClasspathXmlServiceLocator.getBean(WebLocalClasspathXmlServiceLocator.java:69)
        at jetbrains.springframework.configuration.runtime.ServiceLocator.getBean(ServiceLocator.java:54)
        at jetbrains.teamsys.dnq.runtime.util.DnqUtils.initModelMetaData(DnqUtils.java:48)
        at jetbrains.charisma.persistent.InitModelMetaDataServiceLocatorListener.onAfterInit(InitModelMetaDataServiceLocatorListener.java:10)
        at jetbrains.springframework.configuration.runtime.ServiceLocator.fireLocalAfterInit(ServiceLocator.java:112)
        at jetbrains.charisma.main.ServletImpl.init(ServletImpl.java:70)
        at javax.servlet.GenericServlet.init(GenericServlet.java:242)
        at org.eclipse.jetty.servlet.ServletHolder.initServlet(ServletHolder.java:517)
        at org.eclipse.jetty.servlet.ServletHolder.getServlet(ServletHolder.java:402)
        at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:621)
        at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1336)
        at jetbrains.mps.webr.runtime.filter.QueryParameterFilter.doFilter(QueryParameterFilter.java:25)
        at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1307)
        at org.eclipse.jetty.continuation.ContinuationFilter.doFilter(ContinuationFilter.java:137)
        at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1307)
        at org.eclipse.jetty.servlets.UserAgentFilter.doFilter(UserAgentFilter.java:82)
        at org.eclipse.jetty.servlets.GzipFilter.doFilter(GzipFilter.java:242)
        at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1307)
        at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:453)
        at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:137)
        at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:559)
        at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:231)
        at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1072)
        at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:382)
        at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:193)
        at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1006)
        at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:135)
        at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:116)
        at org.eclipse.jetty.server.Server.handle(Server.java:365)
        at org.eclipse.jetty.server.AbstractHttpConnection.handleRequest(AbstractHttpConnection.java:485)
        at org.eclipse.jetty.server.AbstractHttpConnection.content(AbstractHttpConnection.java:937)
        at org.eclipse.jetty.server.AbstractHttpConnection$RequestHandler.content(AbstractHttpConnection.java:998)
        at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:856)
        at org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:240)
        at org.eclipse.jetty.server.AsyncHttpConnection.handle(AsyncHttpConnection.java:82)
        at org.eclipse.jetty.io.nio.SelectChannelEndPoint.handle(SelectChannelEndPoint.java:627)
        at org.eclipse.jetty.io.nio.SelectChannelEndPoint$1.run(SelectChannelEndPoint.java:51)
        at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:608)
        at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:543)
        at java.lang.Thread.run(Thread.java:722)
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'persistentEntityStore' defined in file [/home/svc-utrack/.youtrack/work/jetty-0.0.0.0-8282-youtrack-5.0.6.jar--any-/webapp/WEB-INF/classes/jetbrains/charisma/persistent/storeConfigurationDatabase.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [jetbrains.exodus.database.PersistentEntityStoreImpl]: Constructor threw exception; nested exception is java.lang.ArrayIndexOutOfBoundsException: 30720
        at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:254)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:925)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:835)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:440)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory$1.run(AbstractAutowireCapableBeanFactory.java:409)
        at java.security.AccessController.doPrivileged(Native Method)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:380)
        at org.springframework.beans.factory.support.AbstractBeanFactory$2.getObject(AbstractBeanFactory.java:302)
        at webr.framework.controller.WebLocalScope.get(WebLocalScope.java:33)
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:298)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:185)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:164)
        at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:269)
        ... 53 more
Caused by: org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [jetbrains.exodus.database.PersistentEntityStoreImpl]: Constructor threw exception; nested exception is java.lang.ArrayIndexOutOfBoundsException: 30720
        at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:115)
        at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:87)
        at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:248)
        ... 65 more
Caused by: java.lang.ArrayIndexOutOfBoundsException: 30720
        at jetbrains.exodus.log.LoggableFactory.create(LoggableFactory.java:34)
        at jetbrains.exodus.log.Log.read(Log.java:389)
        at jetbrains.exodus.log.Log.read(Log.java:369)
        at jetbrains.exodus.tree.btree.BTreeBase.getLoggable(BTreeBase.java:101)
        at jetbrains.exodus.tree.btree.BTreeBase.loadLeaf(BTreeBase.java:136)
        at jetbrains.exodus.tree.btree.BasePageImmutable.compare(BasePageImmutable.java:126)
        at jetbrains.exodus.log.RandomAccessByteIterable.binarySearch(RandomAccessByteIterable.java:159)
        at jetbrains.exodus.tree.btree.BasePageImmutable.binarySearch(BasePageImmutable.java:119)
        at jetbrains.exodus.tree.btree.BasePageImmutable.binarySearch(BasePageImmutable.java:111)
        at jetbrains.exodus.tree.btree.BottomPage.find(BottomPage.java:150)
        at jetbrains.exodus.tree.btree.BottomPage.find(BottomPage.java:49)
        at jetbrains.exodus.tree.btree.BTreeTraverser.moveTo(BTreeTraverser.java:208)
        at jetbrains.exodus.tree.TreeCursor.moveTo(TreeCursor.java:224)
        at jetbrains.exodus.tree.TreeCursor.getSearchBoth(TreeCursor.java:189)
        at jetbrains.exodus.env.CursorImpl.getSearchBoth(CursorImpl.java:100)
        at jetbrains.exodus.database.PersistentEntityStoreImpl.refactorMakePropTablesConsistent(PersistentEntityStoreImpl.java:2303)
        at jetbrains.exodus.database.PersistentEntityStoreImpl.applyRefactorings(PersistentEntityStoreImpl.java:238)
        at jetbrains.exodus.database.PersistentEntityStoreImpl.<init>(PersistentEntityStoreImpl.java:187)
        at jetbrains.exodus.database.PersistentEntityStoreImpl.<init>(PersistentEntityStoreImpl.java:118)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
        at java.lang.reflect.Constructor.newInstance(Constructor.java:525)
        at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:100)
        ... 67 more