This is just a guess but it seems like you are not creating the features in your Mobile App correctly.
Maybe there is something wrong with your code?
How about making a mobile project using the Project Center and creating quick test application.
I do this quite often to test new features with certain feature classes.
I personally don't register my feature classes as versioned.
When I sync I have no problems. However, I am still using ArcGIS 10.0. We have some plans in the future to move to 10.1 or 10.2.