From what I can see, they are correct. I don't see anything that would trigger a malformed manifest error.
A similar error that I noticed (and now fixed) is that the bootstrap would attempt to load the FileCatalog.sbfc when it's the first time that the game boots. So, if you have strict cache checking on or disabled the option to clear the cache when the game closes, check out the update.
If not, feel free to send me a build of the game so I can diagnose it.