what version are you running? I have had similar in the past where user machine ID's with special characters caused PGO files to become corrupted and not display correctly in the QMC, like you are describing
Backup and antivirus programs locks the files for scanning
Corruption of the PGO file.
The PGO files (master copy) are saved on a unit that for some reasons are not accessible ex due to network issues. The recommendation to avid this is to have the source root folder on the same machine as the QVS and use mounted folders when needed.
Heavy I/O to the PGO - resulting in locking problems (and possible corruption).
There have been allot of work and improvements done into this area so my general recommendation is to upgrade if you continue to run into issues.