Thank you for the assistance. It's a little embarrassing to admit, but though I thought I had installed the game correctly the first time, after my recent install (just to be sure, I wiped my drive of the game and rome and re-installed it all) I notice the version actually change to 1.2, whereas I had tried to do it right the first time but it remained 1.1 I've applied the optional patches and it seems to be a proper install now.

Sorry for the trouble, I still have that bugged save file, but I think it's best I continue with a new game and see if it occurs again, in which case I'll follow the above directions and see if it is indeed a rebellion to cause it.

I appreciate your time.