Just a thought.
But rather than having the autosave occur at the start of the following turn, wouldn't it make more sense for the save to be made at the 'end' of the previous turn, i.e. saving before they clicked the end turn button?
That would solve all these issues right there...
Admittedly, the would have to recode the autosaving mechanic, but it would be easier than trying to try to figure out where the bugs are with the current mechanic and fix them.
The negative side, of course, is that it would probably allow for 'save scumming': reload the save, end the turn, and then capture a lair or whatnot and get something new.