Hi Rick;
I had a similar experience when migrating my STD framework and demo Apps to R2. Some things would not work even after performing a full build (which I recommend everyone doing before running your apps anyway). The problems started after running the App's right after the full build from the IDE and was also present in the EXE's.
The way I got around this issue was to use PB's "Object Browser" located in the IDE. For the Menu, Window & User Object class's, I regenerated from the top level object in each class area all the way through to the lowest level descendants. The PB IDE's full build does not rebuild the object classes in their ancestor sequences thus, may not pick up code realignment as you move from descendant to descendant. Whereas the object browser regeneration does! ;-)
After the object browser re-generations, I then performed another full build and now my apps all work again. What I'm doing now is performing my own full regression testing under R2.
HTH
Regards... Chris