What am I doing wrong here? (Bag issues)

I have spent the last 50 years or whatever just using the individual bag UI; where I'd set one for equipment, one for junk etc etc.

I decided to finally enter the brave new world of combined bags becasue I'm now an adult and dispite setting them all to just 'everything'... the system still make random little arrangements when I loot stuff. It also highlights a bunch of totally random slots blue as if to say "these are all from the same container" - when you mouse over any of them they vanish but still, wtf.

Has something gone horribly wrong? Shouldn't it just stack things right to left, top to bottom and not be ... doing whatever on earth it's trying to do?