Yeah, the first time I open everything when I first log in a character, those first few minutes in-game are usually spent moving bags around and getting everything adjusted. After that they tend to stay where you wanted them... at least till the next time you log that character in.
Since I usually start off at the bank anyway, I try not to let it bug me... but if someone is extremely **** about placement, I can see where it could be a real issue for them...
What really got to me was the way labels didn't stick to bags and boxes for a week or two after they added the label feature... For a while there, it seemed like I was labeling all my strongboxes and backpacks every time I opened them!