Yes, scout movement is the whole problem here. Never got it on a AT before, though. The scout movement allows the unit to move a bit like a recon - meaning you can move your unit agin after you made a move. Applied on a AT, AA or Artillery (not sure if these all could get that skill), the programm forgets that they can't move on their own, and doesn't load and unloads the unit.

You can try to do this manually. If I remember correct it is the rightmost option on the reference card of your unit where you can also ask for reinforcements and refuel/reammo the unit, and then afterwards move the unit to it's destination. Due to the scout move skill, you might even be able to unpack (unload) your unit at the destination hex instead of being blocked it it's transport and thus prone to attacks