I was just trying to replicate what you've mentioned. For me the highlighted search criteria only stays highlighted when the search tab is open AND the search criteria is still in the search history. As soon as it's removed from the search history or the search tab is closed the highlighted occurances in the code are removed. This is the behaviour that is expected.
From what you've mentioned I've understood that the occurances stayed highlighted even after closing the search. Firstly a real simple question, have you got the critieria highlighted with the cursor? By default the search occurances and the "normal" occurances are the same colour.
Other than that it sounds like you may have some sort of corrupt preferences / install, maybe a workspace refresh will work, if not and if it's worth it, do a re-install.
Thanks for the response, Ollie Edge. I don't have the criteria highlighted with the "normal" cursor. The expected behavior you describe is precisely how Flash Builder used to work for me.
This may be a long shot, but the problem seems to have started after I used Remote Desktop Connection to log into my work computer from home (the problem is happening on my work computer). Perhaps the issue has something to do with searching Flash Builder over Remote Desktop Connection. At any rate, I'll consider trying a new workspace and/or reinstall.