I figured out what is causing aberrations in the variable-geometry wings of the F-14 Tomcat and VF-1 Valkyrie. The origin for the wings is in the center of the model--this is incorrect. Each wing should rotate around the point where it meets the body, but instead it rotates around the center, in between the wings.
This causes the abnormal rotation. Fix the centers of rotation and it should work properly. The "swapping" thing in PCS2 is irrelevant because both wings have the exact same center of rotation in the current (bugged) model. In fact, the whole swapping thing isn't even real--open it up in modelview and the bounding boxes are right where they should be.