I ran into this same issue. There was an issue with the cache state and it not overwriting the orginal storage. Mine was a bug that when you have set it for stateful and then go to stateless the rebuild will not overwrite the original install. This then prompts for a reboot to put in the correct mode. I did also have a stateless caching issue in my host profile complaince check. Format the storage the host is installed on and then reboot and let the stateless/stateful caching rebuild your cache. Also, what settings are you doing for your caching?
If you can provide a little more detail of how you have setup your autodeploy I can try it in the lab and see if I can figure it out.