OK! With the plane right side up with the wheels off the ground, engine off, do the retracts work correctly? If so, then what about lifting the aiplane up off the wheels with the engine runing, but not flying and see what happens. I'm just wondering if some vibration from the engine may be causing problems in either the retract servo, or Y harness, or receiver. You might want to try to mix the two servos in the radio. That's what i have done but i haven't run my engine yet so I'm not even sure if I'm going to have the same problem as you. I might
You Just need to see if you can duplicate the problem on the bench before flying again.
Jim