You may have two issues here or perhaps one?
(1) With 3 radio cards onto one MT device can cause interference between the radio cards and the proof is as you say when data increases the throughput collapses, I have a simple policy, 1 radio card = 1 Routerboard also integrated Antenna’s gets rid of RF leads (LMR400, etc.) so the losses from radio card to antenna are reduced, also in your present setup if the board goes down you lose 3 radio cards and customers connected to those cards,
(2) Co- location interference pickup when one antenna picks up signals from the other antennas on the mast, have you done a signal scan from each antenna and checked if the results show signals below -30, I had problems with antennas on a mast with this but solved it with RF screening.http://forum.mikrotik.com/t/radio-card-rx-bandwidth/45267/1
(3) When you say “All my other setups are very similar and don’t do this….” Are they using exactly the same hardware, same distance apart + position on mast, same frequencies, etc. if not then they cannot when RF is involved be considered “RF similar” but appearance are.