Doesn't save PHPR file

I've noticed that sometimes after doing the BUILD, it waits on the final page for my FINISH command and then "usually" prompts me as to whether I want to save the PHPR file.
Lately, howver, about half the time it doesn't ask me if I want to save it... and it DOESN'T.
Is there something that triggers whether to save the PHPR or not? If I just tweak changes in the Visual Editor does that NOT get reflected in the PHPR? I'm afraid that I'm going to be missing some changes when I go in the next time.