Will adding reverse protection diodes across the current limiters cancel this out.
No. When you run the motors there's a likely hood of generating large back emf from the stepper coils the diodes are to stop this damaging the LM317s.

That looks like a normal rectified transformer output. Ripple is, what?, 3v - perhaps a bit high for a few amps of load. What size (VA) transformer and smoothing cap?