I too have a 4xEIDE interface on my A1200, though I'm running it under OS3.5. I just installed a second hand CD drive (non-writer) and I too have noticed a wierd clunking noise from it when I boot up. It almost sounds like the computer thinks it's a floppy drive...
Anyway, it works fine despite this, reads CDs with no problems and so far has not shattered any CDs...
However as I cannot afford a tower I have the CD drive strung out the side of the A1200 with it's own power supply. I have noticed that I cannot boot unless the CD drive's power has been switched on for a few seconds before I turn the computer's power on. Switching them on simultaneously will not work, which I assume would the situation in your tower. Perhaps this is part of your problem.
I also have a ZIP drive which I sometimes in place of the CD drive and the above is all true for this as well, so I'm fairly sure that it's something to do with the 4xEIDE interface rather than my drives.
