Hm, let me explain the problem.
Guest customization is always delivered to the guest OS in a form of package. There are 3 types of packages: unix_deployment_package.tar.gz (used for Linux OSes), windows_deployment_package_sidgen.cab (used by Vista+ and XP/2003 [only in case "Change SID" == false]) and windows_deployment_package_sysprep.cab (used by XP/2003 only in case "Change SID" == true). On the clean install you don't have any of them. Documentation has instructions on how to create the third one, because VCD can't generate one automatically. But it's only needed if you have XP/2003 OSes, otherwise VCD can work without it. The other two can and normally are generated by VCD automatically. Once they are generated, they are used as some sort of cache. In other words VCD will never try to regenerate them again. So, it's a problem when you upgrade - the bug is that VCD doesn't regenerate the packages and keeps using the old code.
The fix of deleting all those packages went into 5.1.2 (+ a warning that you need to regenerate windows_deployment_package_sysprep.cab [if you had one] manually).
So, you can try to:
- backup the old files
- move them somewhere else
- run customization of Linux and Vista+ VM to get those regenerated
If something goes wrong, you can always put back the old files and VCD will keep using them.
/Andrii