When you have two drives on one IDE cable, only one drive can be active at a time. So the data transfers have to switch back and forth between drives. If you're doing a heavy data transfer on one drive, it may end up using a larger proportion of the access time and the operating system's attention.
If they're on different cables, then it's probably just the OS having too much attention taken by the big transfer. The type of IDE controller and driver used can make a big difference. The CPU may be heavily involved in the transfer, which UltraATA is supposed to reduce but some drivers and controller types don't do it so well. (For example the nforce2 IDE controller, some people see 35% and higher CPU usage when using hard drives.)
SerialATA only allows one drive per port, so there shouldn't be any issue with one drive hogging the bandwidth. However bad drivers or controller design could still result in heavy CPU usage.