Well first off the Bohing vanes (especially the high profile versions) are noticeabley heavier than the AAEs. this may cause high and low shots... with broadheads especially.

Also the materials they are made of (polymer vs. rubber) are quite different and may very well react differently at the shot (especially if you have a contact issue since the AAE's tend to deflect less)

The Bohings due to their higher profile may CAUSE a contact problem at the rest or cables.

Nothing wrong with Bohning vanes but each and every arrow in your quiver should be as close to the same as possible if you want consistent accuracy.