If you have pictures of each end showing antenna alignment, cabling and connections to the APs, etc, that will help. You are sure the cables and connectors are 100% tight, there are no sharp bends in the cable, etc? What is the type of antenna cable (LMR200, LMR400, etc)?
How are you testing throughput or are you just looking at the link rate? Can you get the show tech from the MSR2K and MST200 and send them to me at jhoward *at* arubanetworks *dot* com?