Can you post your assemly and parts in a zip file? It's hard to know exactly what is happening here without seeing the model.
I'll venture a guess that some assembly constraints are the cause of the trouble. Is the problem only with the two support angles that are on the curved faces? How did you constrain them to your skeleton? Edge to edge?
Hi! If I understand this issue correctly, it is about the frame members misalign when reference source geometry tranforms in the model space. This is a known limitation in R2012 unfortunately. The issue here is that the frame member is not aware of the alignment. When the reference part changes shape resulting in relocating the frames, the frame alignment may not adjust accordingly.
In R2013, Frame Generator provides Align option. If a member is edited, you can pick an alignment reference (plane or edge). Then as long as the alignment reference geometry exists, the frame should align accordingly.
Johnson Shiue (email@example.com) Principal SQA Engineer, Inventor Manufacturing Group Autodesk, Inc.