This is happening even without anyone deleting the database? If the file is deleted and not recreated, the file will be recreated with a size of 0 but won't really be the db, ready to work. I would suggest upgrading to a current Service Pack for any fixes that may help with this. You could even just try it out in a test environment. Another option would be to see if anything else has the policy db file open. The log is saying it timed out trying to get access (the mutex) to the db file. Maybe something is running? Maybe an AV or something is grabbing the file?
Thanks for the update ,
Yes it is happening even without deleting the database file. Let me disable the AV and test in our test environment , I will come back if I can reproduce the error in test environment.
I had the same issue at one of our customers. The problem was, the db clean up script that tries to recreate the local db points to the "c:\program files..." folder. This didn't work on a 64 bit OS because all related files are under "C.\Program Files (x86)...". We had to create another script that points to the correct program files folder for 64 bit and created a second policy clean up tasks for these devices and everything works fine.