You might try clearing your workspace. It sounds like you have a bad cache in there somewhere. Quit Flex Builder and then delete the .metadata and configuration folders in your workspace (but not your projects). You can then reimport your projects when you re-launch Flex Buider. The easiest way to find your workspace (if you don't know where it is) is to launch FB and choose Switch Workspace. The path shown is your current workspace. Then just cancel out of that dialog, quit FB and follow the steps above.
Hope that helps, -Heidi
