Hi again,
I have just found out that I have another save that is affected. Its the 10.53 am one, also I added it to the dropbox. It seems that only my main character, the dwarf barbarian, is affected. He does start off with being charmed, so that might be a factor. It also seems to be only the saves on level 8 and 9 of od nua. He also seems to not want to be selected at the start with the select all button until you click on him manually even when the charm has ended. I have tried to recreate the issue, but I have just managed to clear level 8 again without encountering the issue. I think the issue must begin with the earliest save, the 10.53 one.
Well I can get past those sections now so I'm not too worried anymore. I'll just continue on like it never happened. I'll keep the saves and that just in case. When you don't need the dropbox stuff anymore just yell/post in this thread, I'll keep a eye out for it.
Finally
MERRY CHRISTMAS!!
p.s Also a small bug I just remembered, when I first start pillars and load into a save, when I first look at the stronghold actions tab/section the quest section always says assign even if someone already has been. If you click on it it does the recall. When you switch out and back into that section it fixes itself and says recall.