That's odd. I used UCD today for a station building project. Shuttle Fleet carries an Artemis node, with UCD as Atremis_temp with Atremis as it's core, used UCD to "dock" a PMA to Artemis dock 1.
Once I arrived in orbit, used the RMS to position the PMA above the shuttles docking port. After I'd noticed that the two would dock properly (although I got the docking sound, and scenario editor said they were docked, the objects would pass through one another.
I grappled, again, and lined up to the docking port, again. Then used the scenario editor to delete Artemis_temp. The docking ports snapped into position like they should, I released the cargo with the RMS, and proceeded with the mission.
Shuttle Fleets autopilot worked fine, but I've not tried it upon reloading a scenario. Do you mean one with from a quicksave? or a 'current scenario' reload?
edit...
I ran the scenario again several times. It seems like I'm getting the goofy autopilot gripe you mentioned, but not every time. Say maybe 25% of the attempts. When it works, it works, when it doesn't the shuttle may wind up trying for a retrograde orbit instead of where it's programmed.