Just to clarify - you're talking about File > Save when editing controls in the PB IDE, not when your compiled app is doing a Save to the backend database. Is that correct?
Assuming it's saving within the IDE:
Do you notice the same behavior in all the editors? Window, menu, datawindow, NVO, structure, etc...
Is your project under Source Control? If so, which SCC vendor?
Check your library list. Anything strange there? Some PBLs on a shared drive (bad practice BTW - everything should be local), vs. a local drive?
-Paul-