I decided to to file a number of bugs for issues we have been seeing with flex builder. I have posted them here in hopes you will go vote for them. This is only some of the many issues we are seeing using Flash Builder.
Allow multiple instances of an AIR app to run at the same time. - There was a previous issue for this which was closed, so I created a new issue with more details.
Flex Server ate my bin! - This bug was already in the system, but looks like it is stuck on waiting on Info - Hopefully voting on it will get it moving.
Should be able to navigate into script source with Go to Definition Looking through the bug database it looks like several of the renaming bugs have recently been fixed, so maybe renaming will work in the latest release.