Issue with debugging Flash Pro CS6

I have a project I am working on that was created in CS5.5 targeting iOS. The SWF has a lot of content, but no code and the .AS file has all the code except for a few utility functions. I just updated to CS6 and now debugging no longer works as expected. When I run the app in Debug - whether using the mobile or desktop Air debugger environments, it fails to recognize the .AS file as having executable code in it. In CS5.5, when I did this, the AS file would open and I could set and clear breakpoints. Now, if I go to the file and try to toggle a breakpoint, it shows "No exectuable code..." no matter where I set the breakpoint. The app is running fine, but it acts like there is no link between the source file and the app.

The app builds and runs fine - I just can't debug it. Help!

I am sure this is some stupid little thing I haven't done, but since I changed nothing between CS5.5 and CS6, I have no idea where to look.

Scott