Did you used to have another scsi device attached to the end of the chain? It's possible that if you did the termination is not present anymore. I use a warpengine with the scsi controller. I have a CDRom at the end of the chain with a big ol' physical terminator at the end. When I boot up with the CDROM turned on everything boots fine. If I turn on the system with the CDROM turned off I get nothing. Then if I boot from a floppy I can see the drives (like you described) but it won't boot from them unless the CDROM is attached and "on" at the end of the chain. In my case I believe this to be a termination issue. Have you looked into termination on your chain?
