So while playing around with my test-script I opened two shells and ran my script from each. I found out that you get an error in case two processes use the same Perl-Storage. I expected that. But every time I reproduce this error the Perl-Storage is 0KB for a period of time. Depending on which script gets the access it happened that the file was cleared. So this is exactly what might happen in our system.
I added debugging and error checking in our production environment. I'll deploy this on Monday. I'll keep you updated if we could make sure it's the "store" from different processes. If we can confirm this the second step will be to rework this script to avoid this.