I think the same that Michael laenen says about your possible problem. Try identifying in your system any software that can automaticaly delete files. For example some antivirus software, antispyware software, and others similars softwares that can be doing the pgo file deletion. Then you should add to each software a rule to exclude the entry qlikview server folder of the software analysis (C:\Program Data\QlikTech for example)
Do you have an antivirus on the server? if you so as Guzman suggested exclude the antivirus scanning from ProgramData\Qlikview, why? other than deleting them also it locks the file from writing and reading, specially the BorrowCalData.pgo gets out of sync from either root folder copy ( active ones) and Qlikview\QlikviewServer folder ( backup ones). So when one of the PGOs are out of sync, the assignment CALs that you see on the QMC reminds in memory; however, when you reboot the machine, that memory gets cleared and CALs assignments are gone, because the QMC cannot read those PGOs anymore ( due to the lock).
Giuseppe Novello Qlik's Principal Technical Support Engineer