LEDs sharing negative output from driver issue
Figure 1. The pinout for pins 1 and 2 suggests that there are some internal constraints and that there is switching between -Vout and -Vin.


  ... it is a last resort to modify the boards they are on by separating the grounds.


If the LEDs are common cathode then switching the grounds won't work.


  The banks are never supposed to be on at the same time. When one turns off the other turns on and both are supposed to dim up or down at the same time.


There's a conflict in what you are describing here. If they both dim up and down at the same time then there must, at least, be some overlap when they are both on.







simulate this circuit &ndash; Schematic created using CircuitLab

Figure 2. Equivalent circuit. The PWM switches are most likely to be in the LED negative leg.

I think you can't fix this with those power supplies.