Hi Maik,
I don't really know what is the exact cause of your problems, but can offer the following:
You can get the latest programming files from pemicro.com for P&E, not sure about Softec.
You could also get them from a later CW version and still use them with your older 5.0 version. There are no checks done at this level.
As I have noted elsewhere you can just use the GT16A P&E algo for both GT16 and GT16A. If it weren't for a bug in the GT16 version that was exposed by changes in the GT16A there would have been no need to update it at all.
I have devices in prototypes that have probably been re-programmed 100 times with no noticeable differences. This is using P&E USB multilink and P&E stand alone software (which is essentially the same as contained in CW.