Really stuck now!
followed quite a few suggestions from here and pretty much giving up now.
Problem I have is I managed to remove the admin account and cannot get root to 'reset' back to the right privileges.
YT 6 just upgraded from YT 5.2.5
It's installed on a windows server via MSI
Tried the following:
1) Added '-Djetbrains.charisma.restoreRootPassword=true' to youtrack.jvmoptions in C:\ProgramData\JetBrains\YouTrack\conf\
2) sc start youtrack -Djetbrains.charisma.restoreRootPassword=true
I'm out of ideas, I even read this: https://confluence.jetbrains.com/display/YTD6/Changing+or+Restoring+Password+and+Permissions+for+Root
and that didn't work either, YT6 seems to be really broken, or just the reset feature hasn't been tested with the new db upgrade?