If I sit and watch it work it says "file not found" when it get to the fixwindows action that is in the template preceeding the inject. The path is correct though and the file is there. Manually running the file yields the BCD not found error though which I think is what the template error is supposed to be reporting instead.
I've given up on relying on fixwindows though and have bheen working with a manual make active and assign actions to get the C drive mounted instead. Now its simply a matter of solving the issue with the CTOS hanging 20% of the time.