Some harddrives have specfic settings for if they have a slave on the same channel or not. Perhaps your old drive was set to have a slave, but it didn't. Though usally the drives just plain won't work. In the case of a Western Digital I delt with, it would start to boot then give a blue screen untill it was set to single.
Wouldnt it be true that your existing info is stored on your current drive which should run at its current speed and the other drive ATM makes no difference at all for now? Your computer will run faster (if program dependent) if you add more RAM, a better CPU and a faster HDD (providing your files are stored on there in the first place). If you add a drive then at the beginning nothing should be on there and you PC should run like it was.
you should take the harddrive out and see if the computer slows down. If it does, well then..it'll be wierd. How much space do you have left on your old harddrive?
and btw...that title of yours is very misleading, especially to computer noobs...