I was curious about this stuff, all the master and slave talk, and wondering why the 80 conductor cable was an issue, and after some digging found these links:

http://www.pcguide.com/ref/hdd/if/ide/confCable-c.html
http://www.pcguide.com/ref/hdd/if/ide/conf_Cable80.htm

My PC's BIOS is smart enough to detect and display (at bootup) if an 80-wire cable is present or not. It must have been deliberately throttling the drive because of the lack of the 80-wire cable, hence the issue.

I can't find anything in there saying that the drives in a master/slave configuration "must" be physically positioned a certain way. What I do see is that if you're using cable select then the master/slave configuration will come out that way but I can't find anything stating that two drives on the same cable must be that way.

One thing they do say is that if you're running one drive all by itself, then you shouldn't put it on the middle connector. Leaving the end connector dangling makes it pick up EMI interference like an antenna. Hmm... our beloved Mk2 is that way by default...