Though this technote may be a fix, just trying to get more insight into it. How are you clearing backmode? From GUI or powershell cmds?
try this if not already tried from .bazt script:
C:\........\powershell.exe -PSConsole "Path to Enterprise Vault Install Folder\EVshell.psc1" Clear-VaultStoreBackupMode EVSITENAME EVJOURNAL1 Site
C:\........powershell.exe -PSConsole "Path to Enterprise Vault Install Folder\EVshell.psc1" Clear-IndexLocationBackupMode EVSERVERNAME -EVSiteName EVSITENAME
*** Put correct values for items in bold.