Without seeing it, I'd take a guess that it could be a deformation order thing.

Next to the magnet icons in the status line (the snapping tools) are a couple of buttons labeled Inputs and Outputs. If you choose All Inputs with the selected object, you get a list of all inputs for that object. If you Middle Mouse button drag on those inputs in the list, you can reorder them (most of the time). You can play with this ordering and see if perhaps that helps the issue.