@iGeek
Time ago , but better late than never ...
The problem in your project is, that the rootbone for the cube and sphere is moved . The rootbone is the rotationcenter in A:M. I have correctet this in the attached projectfile. I recommend also to use "Dynamic Object" as objecttype for the sphere , instead of "Static with Action"
@Matt
There is a similar problem with your holed cylinder , the model is not centered at 0,0,0 .
It where good , when you can provide a projectfile , where I can see , in which case the simulation failed .
newton_test.zip