Try it with two brand new X2A projects and if you are running realtime antivirus scan MS recommends excluding:
C:\windows\SoftwareDistribution\Datastore\Logs\res*.log
C:\windows\SoftwareDistribution\Datastore\Logs\res*.jrs
C:\windows\SoftwareDistribution\Datastore\Logs\edb.chk
C:\windows\SoftwareDistribution\Datastore\Logs\Tmp.edb
c:\windows\Security\Database\*.edb
c:\windows\Security\Database\*.sdb
c:\windows\Security\Database\*.log
c:\windows\Security\Database\*.chk
c:\windows\Security\Database\*.jrs
C:\ProgramData\NTUser.pol
C:\Windows\System32\GroupPolicy\Registry.pol
I also exclude the Cakewalk Content and Project folders.
For bug fixes you really need to come to the X3 side I'm afraid, but I'm doubting your issue is exclusively a Sonar issue.