Recently, I quite frequently see IDEA come into a mode where it flags large amounts of my source files as "unused" (yellow color), which they are definitely not. Just now it happened that IDEA even flagged an error which was not actually there.
If this happens, the only remedy is to go to the import section (thats where the unused signs usually start, but maybe its just because its the beginning of the file), and edit a line (e.g., delete and re-insert a character) such that the file gets reparsed - and voila, all is well. Almost feels like someone went to far in trying to optimize the parsing speed (although I still sometimes have to wait several seconds until the IDE becomes responsive)
this is Sun 1.4.1_01 under Linux 2.4