I have a Flex project that I copied in from another source to work on. I changed around some output properties and library paths via the Properties context menu for the project. The changes would hold while Flex was open, but it would never update the .actionScriptProperties file, thus when Eclipse was restarted, the changed would revert.
After doing a little bit of Googling on the issue and not finding much help I ended up making a backup copy of the folder, deleting the folder, and importing the files into the new folder via Flex Builder. This fixed the issue. Not sure what caused this, but it works now.