" CD " seems to be the only command it reconizes.
That's fine, but it seems you didn't get my idea.
If you enter cd without any paramters, it will tell you which partition you currently are on. So please enter cd without parameters imediately after a warm boot attempt and see which partition is your "ghost" boot partition. I guess it is different from your usual boot partition.
I could imagine a scenario like this:
You have two HDDs. The first one contains your normal boot parttion. The second one contains a bootable partition, too, which has a higer boot priority. On a cold start the second HDD is not recognised because it spins up too slow (a common Amiga problem). On a warm reboot both harddrives are recognised and the second one takes precedence because it has the higher boot prio. It shows an empty DOS window because it does not contain an operating system.
Bye,
Thomas