Finally the solution
1. The hardware has been OK all along, no problems with the drives, cards, power, or jumpers.
2. The issue was with the fact that the CDOS I was using was configured for an A drive = 5 1/4" and a B drive = 8" !
So that's why it was "not ready" for a 5 1/4" drive in one system yet was fully able to boot in an 8" drive system. I did not know that I had a CDOS configured that way, or better way to say it I did not realize it was even an issue.
Thanks Marcus and Mike S for your help.
So what you do is run the command CDOSGEN after booting the disk, and follow the prompts to build a disk that is compatible with the drives you have. It never occurred to me that this was necessary. Note that I backed up the original disk using RDOS first, and updated my copy using CDOSGEN, just in case something went wrong.
Here is the thread from the Cromemco Google Group:
http://groups.google.com/group/cromemco/browse_thread/thread/9f180f5f17b7a009#