That is strange... I have hard time to guess how they can interfere.
Well, you can try to use my plug-in instead of original for FaderPort:
http://www.azslow.com/index.php/topic,163.0.htmlSo far there was no reports that A-Pro is not working with other plug-ins, especially I know that some people use it with my (controlling other device). Also there are people which say that FaderPort works with my plug-in better then with original (but some other claim it does not work with my plug-in at all...).
Also make should that Input/Output assignments for both Control Surfaces are correct. So you do not set output of A-PRO to Faderport (just an example). Note that you should have only 2 plug-ins in Control Surfaces, one for each device. If you see more, remove them.