Hi Ryan,
I just had a similar issue – 2 mograph cache tags in one project and only one would bake. A few restarts later and it cleared itself up. Still don’t know what the problem was.
We’re having a terrible memory leak issue here. On machines with not quite enough ram to do the rendering, Cinema brings them to their knees when the rendering is done and a number of restarts are required to clear the ram and the page file before you can do anything else (Cinema or otherwise).