What operating systems and browsers do you see this behavior in? Does it always happen or only under certain conditions?
This is consistent, once it was pointed out to me it does it every time I test it. I have tested using Firefox 3 (both Mac and PC) and Safari. Firefox 3.1 beta (Mac) also does it. Haven't tried IE as we don't use it.
To duplicate, use an account with a number of IMAP folders. If they all fit in your window (no scroll bar shown) it works as normal. Drag a message and the destination folder(s) highlight with yellow under the cursor as expected.
Now shorten the depth of your window so that the folder list shows a scroll bar. Make certain to shorten the window enough so that several folders at the bottom of the list are out of view. If you drag while the scroll bar is at the top (default position) it still works as expected.
Now scroll down in the folder list. Drag a message into the folder list. Note that the yellow highlight is several folders up the list. In fact, the highlighted destination folder is above the cursor by how ever many folders you scrolled down. If you scroll down 3 folders, the highlighted destination is 3 folders above the cursor. If you scroll down 10 folders, the highlighted folder is 10 folders up the list. As you can see, it is easy for the highlighted destination folder to even be off the screen and invisible. Worse, if you release the message, it is moved into the folder that is highlighted, NOT the folder under the cursor. This can cause misplaced messages very easily.
This behavior is not evident in the default skin, where scrolling does not affect the correct function. My guess is that the folder list is not being refreshed in some way after scrolling.
In case you can not duplicate this on your system, I can provide a test account on mine, if necessary. I can be emailed at aberglund (at) lesd.k12.or.us