So the codes received "change".. are they random, changing values?
Sounds like electrical interference from the PWM switching.. Maybe.
Try shielding the wiring to the IR receiver and separating it from the motor wiring. Try adding a capacitor (maybe .1uF) across the Vcc and Gnd pins right at the IR receiver.
See the IR info on the ArduinoInfo.Info WIKI HERE:
Let us know what happens; I'd like to add info to the WIKI if possible.