I have a CSMK3 (same SCSI) and a newer 15k Maxtor Atlas. It would not boot either. I tried many different configurations of drive jumpers, SCSI chain order and terminators, and CS boot menu (ESC) configurations. I have the latest flash for the CSMK3 and AmigaOS 3.9 also. I finally found one way to make it work. I put another SCSI device at the SCSI address before it. In other words...
SCSI address 1 Compaq HD (with active termination, physically at end of cable)
SCSI address 2 Maxtor Atlas 15k HD (with boot partition)
Normally, I would want the HD with the boot partition at address 0 and the small hard drive could be removed and replaced with an active terminator, but this did not boot. I still get a guru the first time I turn on my Amiga but after it reboots I have a fast and stable Amiga. I get about 30MB/s sustained. The synchronous flag has to be set in the RDB or forced in the CSMK3 boot menu. If anyone has a better solution, I would like to hear about it.
