I mounted the motor with hard drive magnets instead of bolts like before - this may be resulting in less agitation. Before I change this I will up the current to the motor and see if that works (or shakes it right off).

Also, the new enclosure is amplifying the vibration noise like a guitar body. I will try a silicone gasket (made from a silicone baking mat) to see if the reduces the noise a bit.