Not sure if it is the same/related, but there are some issues that I have reported about (some time ago - had hoped for some fixes by now) when recording/playing back with a DAW and using PolyBrute Connect. This was with Cubase and, of course, you have to remember to switch on the recording and play back of control information.
Specifically, what I found when I had a split preset with a sequence plus a mophable pad was that the Morphee information (I was using it for ratcheting for a sequence) was captured and played back OK if (and onlky if) using PolyBrute Connect - but when using PolyBrute Connect, the morph control knob (can't remember the CC it used) was getting ignored by the PolyBrute. If you connected just as MIDI without PolyBrute Connect, then the Morphee information was not capture/replayed but the morph control knob CC was working. It seems as if the PolyBrute changes what it recognises/sends based on whether it is connected over MIDI or through PolyBrute Connect.
I found that I could record everything in one take, but if I wanted to make changes, then I would have to do multiple recordings back so that I could play the sequence to adjust the ratcheting when connected via PolyBrute Connect, and then separately for the morphing of the pad having disconnected the PolyBrute Connect plugin. Not ideal, and I do hope that this gets addressed as it makes using these features in a live situation where some of it is driven by a DAW almost impossible.