Sorry Robert that's my fault for typing in a hurry. As you said, the SDK didn't come with the source download, I downloaded it seperately and pathed to it in Flash Builder. Sorry I mispoke there.
I figured out the problem. After importing the project initially there were 80 errors reported in the 'Problems' pane. I was expecting those errors to clear after pathing to the SDK but they didn't. Then I renamed the project and that seemed to trigger a reload and all the errors were cleared. Then I exported the release build and it worked.