When they get revert for any chances did you rebooted the machine or restarted the Qlikview services? Can you check in PGO files timestamp are in sync each others.
Active PGOs ( this is normally what you have listed as your Root folder for QVS): C:\ProgramData\QlikTech\Documents
Backups PGOs: C:\ProgramData\QlikTech\QlikViewServer
Both need to have exactly same timestamp and sync, if you have a cluster there you have to check each nodes backups PGOs. If they are not in Sync that means that something is holding it, like Anti-virus ( very common McAfee), Backup systems, etc. For that to make them in sync, you need to recreate them.