flawlor,
Sorry that you are seeing this issue.
Can you please switch to a new workspace, import the project, go through the upgrade wizard ? Do you see any errors post the upgrade?
Restart the IDE, and check if you see the message to upgrade project again. If yes, please send us the contents of the .log file which is located at <workspace dir>/.metadata/.log.
Also if possible, please strip the project of its source code, and send us all the .* files (.class,.settings etc) to help us replicate the issue at our end.