Actually, I found the issue - there's a longstanding bug that seems to still be present. Basically, I have my applications folder set up as a custom folder (I needed more than the default's 3 levels of subdirectories), and arbitrarily QS seems to completely forget all of the items in that folder.
I have to go and manually rescan the folder to get it to reload applications, but after an unknown amount of time, that cache disappears again. I'll try to figure out a reproduce case and file a bug.
