Originally Posted by Prime Junta
@Moriendor and others — It's pretty simple, really: the PATA bus only talks to one device at a time. So, if you have two drives configured as master and slave and move stuff between them, the computer first reads a block from M into memory, then stops reading and writes the block to S. And repeats until it's done.
However, if you have them on separate buses, the system can stream the data from the one to the other — M1 can be reading stuff into memory at the same time as it's being written to M2.
Same thing applies to reading — suppose the game data is on D1 and the swap file on D2, and the system is swapping: it's reading stuff from D1 and writing it to D2, or reading some stuff from D1 and some from D2. Works great if they're on separate buses, but if they're on the same bus, it has to switch between them. You notice this is stuttering, pausing, and lags. IOW it won't affect FPS, but it will affect the length and frequency of stutters as stuff is streamed between the disk(s) and RAM. Very significantly too.
IOW, it's not that they won't work — obviously they will — it's just that they'll work much more slowly than if they're on separate buses.
Don't believe me? Try copying a large volume of data — say, 10 GB — from one disk to another, first with the two disks set up as master and slave on the same connector, then with them set up as masters on different connectors. The difference will be dramatic. I know, because I've tried it, on a fairly recent system too.
Of course, this doesn't apply to SATA. You can plug those in any which way you like.