No, the map differences with BFD2 and BFD3 would not cause this, as they use the same articulations. Ensure you're using the same keymap in both BFD3 and Jamstix, and you should be good to switch out kitpieces at will.
Look at the articulation name in the BFD2 kit and make sure you are getting a 1 to 1 "guess" to the mapping. I was getting some weird mappings on cymbals, but then I realized some kits use "Hit" and all the new ones use "Edge". So even though the map wasn't changing, some of locations were different. Oddly, sometimes you get "hit" in both locations and sometimes you get "edge" in both locations, but not always.
What happens at [current location] stays at [current location].