One thing that gives me trouble is the difference between type filters (selected part type(s?) shown) and mod filters (selected mods hidden). I'm sure it's partly still getting used to the interface, but every time I want to use one of the filters, I have to try to remember which way that particular menu was set up. Well, that and the rather aggressive auto-hiding (if you can't get a toggle to work, maybe it would be easier to implement a delay to allow the mouse to get back on top of the menu?), but it sounds like you're already aware of the second.
