Why does my PMDC motor have spikes in its BEMF?
The spikes are caused by the commutator. As it makes and breaks contact with the coils, the inductance of those coils causes kickback voltages.



That is why snubbers are important on these motors.

As brushes wear the nature of those spikes will change. 

Looking at your curve though, notice that the cyan trace comes up to voltage (current) and "flattens" out within the commutation period while the blue one is still rising when it switches. That suggests the blue motor has a longer coil time constant so I would expect it to give less torque and run slower. 

The reason for that could again be brush related or it could also be something in the magnetics. For instance, if the motor suffered a period of over-heating or over-current. 



BTW: There is no such thing as "two identical PMDC motors".