@ quenthal,
My CyberStorm MK-III SCSI bus goes like this:
68pin Active Terminator - HD(68pin) - CS-MKIII (68pin) - 68pin->50pin converter marked with "ACTIVE" - CD-RW (50pin) - Tape Drive (50pin) - CD-ROM (50pin) - Active terminator (50pin).
Using the built-in termination capability of a device, I have found, is unreliable. Termination power is turned on for all drives that have it available. Built-in termination capability for all devices is turned off. Everything works fine.
A difference that I noticed on your bus is that you have a 68 pin active terminator after the last 50 pin device. That right? Plus, how long is the total length of the 68pin and 50pin cables added together? Maybe it's too long. Also, by the way you describe your drive making noises, maybe it's actually broken in some way that makes it not work with data CDs.