Comp has trouble identifying new harddrive?

Screwed up XP on my old harddrive. Got a brand new harddrive.

Initially had some difficulty getting the computer to recognize the new hard drive; I had apparently plugged it in to the wrong slot on that cord, if memory serves. Switched the plugs, worked fine.

Installed windows. Successfully slaved the old harddrive to the new one, where I could use both in windows XP [Old drive became "F:\"]. Started installing a handfull of things, namely drivers and a couple games. Was running fine for about a week. [If it matters, it was largely still running during that time, with a handfull of shutdowns due to having to install stuff like Direct X.]

Ten minutes ago, I decide I wanna play morrowind, which is located on the old drive. Exited out of the game I was playing, went to My Computer... and the slaved drive wasn't there.

Figuring it was a glitch, I rebooted the computer, only to find out that it isn't recognizing the new hard drive again.

Attempting to reinstall windows [again] reveals that windows is in fact still there on the new hard drive, which doesn't make much sense to me; how can BIOS not know what's attached to it, yet XP can read from it?

Anyway, I have two questions;  one of which being WTF.

The other question is... well, I was told to delete the windows directory on the old harddrive. I didn't.

Could having the old instalation of windows on the old [slaved] drive messed with the installation on the new drive?

That's a tough one, #1.  Forget your computer for now.  Take the 2nd drive (which contains your old files) and put it on another computer of a known-good staus that can accommodate a 2nd drive like that.  Make sure the BIOS sees the 2nd drive.  Get into the drive manager for XP and make sure that drive and its partition (only 1, right?) look OK.  If you can, make sure it isn't set "active", but I haven't done something like that for a while (heck, can FDISK, etc. even unset that kind of thing?).

I hope you understand how the drives should be cabled.  It seems you're using IDE.  Hence, you either do master/slave jumpering, or you jumper both "cable select" and the end drive on the cable becomes the primary.