I couldn't say what is the reason for this behaviour but maybe you could compare the new corrupted one with the older working one if you enabled the extra output of these files as xml within the settings.ini - see here what is meant: Re: Error in QMC " EntLicenses.Properties.calInfo.AssignedList.AddAssignedUsers "
If the QVS cannot communicate with the CalData.pgo file for even a brief period of time (measured in milliseconds), the .pgo file will recreate itiself. When this is done, any info previously contained in the .pgo file is reset and therefore lost. Typically, the most common reason for the communication interruption between the QVS and .pgo file is due to a file lock placed on the .pgo file by another application. Check to see if there are any anti-virus (or other system scanning applications) running on the same server as QVS and explicitly exclude all QlikTech/QlikView directories and filetypes - .qvw, .qvd, .pgo, .shared, .meta, etc.
Hope this helps