Downloaded the source code on both my imac running OS X 10.9.5 and my macbook pro running OS X 10.11.1. I compiled the project for both systems and restarted XCode and loaded up a project with some TODO comments in it. The plugin appears in the menus and everything seems to work ok, yet no actual listing of TODO points occurs in plugin window.
However, if I run the stand-alone app, set the source directory to that same project and add the TODO keywords, the App window lists the TODOs for the source directory correctly.
I'm not even sure where to begin finding out why this is happening.