You can find a list of fixed issues in the release notes, including the template cache issue that I was running into.
Note that your document class in Flash projects should extend org.gaeswf.flash.BaseApplication and your Application MXML in Flex should be of type org.gaeswf.flex.BaseApplication (if none of this makes any sense to you, see my Flex 3 Code Behind Quick Start.)
Update: As of 2.30pm (when I last checked), the app appears to be working again. I've made no changes whatsoever.
The updates in a nutshell:
How cool, I just heard from Brajeshwar on Twitter that The GAE SWF Project is currently the featured application on the Google App Engine Application Gallery.