Thank you again for the suggestion.
After speaking with one of the programmers at our Danfoss distributor, I decided to throw out the pre-made hardware function blocks and build my own. They have half a dozen programmers, and he said none of them use the Danfoss hardware blocks because they include too many unnecessary features and are prone to errors.
After a few minutes of tinkering, I was able to build my own logic to run the PWM outputs. However, I'm getting full signal in one direction and only 25-30% of the end current value in the reverse direction. I'm not sure why that's happening, but I'm guessing that the A output pin is not properly sinking the current when it's flowing in the B to A direction. If you feel like sharing a screenshot of your basic bidirectional PWM pump control, I would love to see it. I totally understand if not.
Thank you again for the help!
****Edit: A little bit of searching led me to this thread, which shows a good example of a bi-directional PWM driven circuit that is nearly identical to the one I built. I'm guessing I've got something set up wrong with the outputs as I was trying to use them all in PinConfig 4 instead of using the H-Bridge pin configuration 8.
https://www.plus1forum.danfoss.com/index.php?topic=803.msg2339#msg2339