when it's retracted is it locking? It could be that you are at the limit of the retract, try shimming the outside edge of your retract unit so that when the gear goes up, it does go into the wing, it will only take probably one washer under the outside of the retract mount to tilt it in a bit.

You could also try bending your gear legs in a little bit though this might interfere with the retract housing itself.

What brand of retracts are they anyway?