Another one thats hardly a big deal, but when typing paths into some prefs fields (File Operations / Double-click on Files) clicking away from the popup suggestion (empty dialog space or something) doesn't dismiss the popup? Again, hardly a priority issue, but visually a bit odd.
The popup will close if you give focus to anything else, e.g. click on the list or any of the other options or another window but not on the background.
(Same behaviour with the pop-ups everywhere, I think, just there's not usually a big background area to click on and notice it. But e.g. click on the "Go" label on the left of the FAYT field when typing a path into it and nothing happens there either.)