Google released version 1.0.2 of the Google App Engine SDK two days ago. If you're using Google App Engine, you should definitely upgrade.
You can find a list of fixed issues in the release notes, including the template cache issue that I was running into.
Also, it's not in the release notes but I just confirmed that the app.yaml skip_files issue has also been fixed. So you don't need the patch any longer.
I also tested the latest version of The GAE SWF Project and it works out-of-the-box with version 1.0.2.