In my experience, its a good idea to use a lower voltage motor when mounting on the subchassis. When I experimented with a back emf supply with higher voltage Maxon, there was a lot of breakthrough. Bringing the speed down fixed the issue.
How is the long term speed stability? My experience with the original pink fish board, was the speed had to be tweaked on a regular basis.
It may also be worth experimenting with the commutation noise filter, if you have not already.