Stray thought, may be way off base.
Sounds like the PMA is messing with the MPPT.
Any chance the wiring between the batteries is a bit too small?
Or one of the battery terminal connections is not as good as it should be?
No idea what kind of PMA you are using. Or where the rectifiers are. Or anything else.
If it is a single or 2 phase PMA, and the rectifier is near the PMA (not near the battery), it may help to add a large capacitor over the DC outputs at the rectifiers.
It is one of those things a simulation will probably not see, but I know I can measure the AC component and frequency at the battery terminals with a cheap meter. If it can be measured with a cheap meter, there is a strong possibility the MPPT controller can see it too, which could confuse the controller to no end.
G-