[Looting Priority]

Same. This confused me a lot. Not just looting, but speaking. If my Main has the high Perception and Lore, I want them doing the talking, not my Rogue.
Clarification please.

[Disappearing Quests]

Likewise lost everything. I had completed everything save the Noble's daughter, but I had reloaded to try not to break the Dragon's egg. When I got back to town and the Herbalist had no idea who I was i checked and saw all my journal entires had vanished, even though i still had all the quest items.

Also that item dissapearing bug is annoying. I didn't notice it until halfway through my playthrough, but once it started it was like gremlins were constantly rifling throuigh my stuff, even equipped items. Pick something up, put it down, *poof* gone.

[Formations completely off-grid]

Not quite the same issue, my custom formations worked in shape, but spacing was odd. So for making a [ shape, I would have L, a gap, and the two characters forming the - on top.

[Cloak Clipping]

Happened for me too. Cloak hanging in the air above BB Rogue's preview.

[Mousewheel 'zooms' parts of the scene]

This happened to me when fighting Nhyre(?) the accused murderer in the Inn. Ghost copies of the characters, along with one of the doors, were created and moved and enlarged as if zooming in, but thye rest of game stayed fully zoomed out.
I hadn't reloaded the game at that point, I had gone through every building in town first, so lots of transitions.