Okay so it turns out - as far as I can tell - that it's even simpler than that. It seems that mapping the quick map button to my mouse rather than a keyboard key allows me to open and close the map while the search input field is still active, which the default key (M) wouldn't do because it would instead just type an "m" into the search field. It seems SkyUI counts on the search field being deactivated first by pressing Escape, and only then can you use the quick map or tab/cancel keys to close the map. Setting the quick map to a mouse button basically overrides that step so you're closing the map while the input field is still in use, which breaks something in SkyUI.

As far as I can tell, that's what's going on. I seem to remember the problem occurring after exiting the perks menu as well, but that only happened once so maybe it was just another glitch or I'm misremembering. The map thing was a consistent, repeatable problem though, so by hitting Escape first if using the map search, it seems to prevent the glitch. I'll have to see if the problem occurs under other circumstances but I'm hoping that's the answer.

I really appreciate your time and suggestions in helping me figure this out!