we just started using the rouge ap detection and have a question regarding the switchport tracking feature. The AP's do see the rouge APs and also the clients connected to it (frame report). The problem is that mostly the aps have a bridge configuration so we will never see those mac's on our switches. Also the +1 -1 searching the WLSE does when detecting the rouge mac does not help because the fast ethernet of the devices is mostly always in a different range.
How about enabling CDP? I think CDP should track the mac addresses of the devices coonected to it. IF this is not what you were looking for, can you send me a screenshot of the mac address and the details of the switchport tracking output? I think you should be able to see those APs acting as bridge too.