Not sure I can offer any real help... but just thinking out loud here:
Is your issue only when trying to use Auto Retract? In other words... can you raise the gear in Manual Mode?
If so, then yeah... I agree it appears to be software related. But if not... then it would seem you may have a hardware issue. Possibly an issue with one of the cylinders, hoses, or manifolds.
Here is a link to all of the Lippert Tech Bulletins. I did a brief dance thru them, and cant see anything related to just the "auto retract" feature... but maybe they can help.