The transfer clutch is what provides torque to the rear wheels in auto Subarus, similar to the centre diff on a manual.
If the auto fluid is very dirty, or the clutch and basket are worn, it will not disengage properly or not react properly and will bind,
This may be your issue, its called 'tight corner braking' and feel like everything binds up, then lets go, with associated clunking.
The auto has its own seperate control unit, not controlled by the Motec, although it does take inputs from the
ECU