edit .ptf file

Are you using the interface to user logic (IUL) for your peripheral or have you written your own class.ptf file?

If you are using a class.ptf, remember to change that and not the system ptf, and after you have changed it you should remove the component from your system in SOPC Builder and then add it again, to ensure the system contains the new parameters.

If you are just using an IUL the only thing I can think of is to make sure you have closed SOPC Builder before you edit the system ptf, but it sounds like you are already doing that. Otherwise just be careful to make sure the same setting isn't set the other way around somewhere else in the same file. PTF is awful for having the same parameter in two or three different places (WIZARD_SCRIPT_ARGUMENTS is often the culprit) and is liable to cause mysterious problems like this when they get out of sync.

Good luck tracking the problem down!