Thanks for taking the time to look through this problem. I'm not new to Solidworks, but new to motion studies as of about two weeks ago. As the title states, I keep seeing an issue with perpendicular mates changing alignment when I switch from the model to the motion study. This is coming up as I am chasing redundant mates while re-assembling the model for a motion study. 

When I create the perpendicular mate in the model, the mate alignment buttons (directly beneath the the angular mate button in the pane) are grayed out. In other words, if I'm looking to change the alignment of the perpendicular faces in the model, I am unable to. Then when I switch tabs to the motion study, occasionally the perpendicular mate has switched orientation. Editing the mate while the motion study is open does not allow me to change the orientation back - the Mate Alignment buttons are still grayed out.

This does not happen to every perpendicular mate, but maybe one in every ten. I've had some luck deleting the perpendicular mate and replacing it with another mate combination. I've also had some luck deleting the perpendicular mate and putting it back in again (as the same perpendicular mate). As I reach the last few components in the model though, I need to use a couple perpendicular mates that are giving me trouble. Has anyone seen this before? Thanks for the advice.