When you get a chance, open that file you have problems with, go to the View -> Symbol Coloring menu, and see if the "Enable Symbol coloring" entry is checked. If so uncheck it. I suspect that it got turned on just for this file, and is what's making us pause. Symbol coloring does a lot of tagging lookups for what's on the screen to give more specific colors for the source code than just "keyword", "library function", etc... A limitation of symbol coloring is that if the tagging queries take too long, it can block the main GUI thread.
I should have caught on to this sooner, but I didn't know how much of the profile to trust (it ran long enough where some of the counters overflowed), and I forgot symbol coloring can be enabled per-file in addition to at the language level.