I had the EXACT same problem. The step would extend all the way but not go back in fully. Some times it would go in further then others but for the most part it would hang out about 30%.
I replaced the Motor and gear box assembly. Cost was just under $200.00 but I didn't want to take the chance of replacing just motor and find out the gear box is worn out. Figured 12 years of usage , might as well replace it.
Put the new motor and gear box in. DID NOT TOUCH THE WIRING OR CONTROL BOX. After the new motor and gear box the step works PERFECT !! every time !
I'd just plan on replacing the stuff I did.
Before I replaced, this is how far they would go back in.