Sounds like you need to do a clean checkout of the modules branch with git. See here http://rawmaterialsoftware.com/viewtopic.php?f=12&t=7660. Scroll down to the bottom for instructions.
You might want to build the Introjucer from the branch and use that to generate a modules compatible project. Just add any files you already had to the project once its created, or reload your old Introjucer project if you used one.