Digital Potentiometer and Motor Speed Controller
The MCP42100 does not appear to be an appropriate digital pot for this application. 

Without a schematic of the motor controller it is hard to tell, but a good guess would be that the digital pot is seeing voltages higher than the supply voltage you are feeding it, and higher than the maximum supply voltage of the digital pot (5.5V; 7.0V abs max). I don't see a voltage regulator on the motor controller board, nor would one be necessary for a low-end design. Probably just a PWM using a 555, as you say. 

To make this work you probably need a different type of digital pot - one that can accept logic level inputs and has a higher supply voltage (12V + some margin). You also typically actually have to feed it the higher supply voltage (and be careful that nothing shorts and ruins the micro board).  

Otherwise the input protection networks on the digital pot conducts more current than you would expect.