I tried to install Fedora core 6 without first running the "Media check". Unfortunately, the disk was corrupted. I ended up screwing up my partition table on one of my disks. So, I reformatted. And then I re-installed windows to my IDE disk. Except, windows will not boot unless I disable my SATA disk. ARGHH! I don't know what to do really. Except maybe try re-installing windows again but I am not sure what that would do. What it comes down to is:

IF YOUR COMPUTER WORKS, DONT F*CK WITH IT! (I learned the hard way )

Okay, I guess I will just have to buy a USB<->SATA adapter.

Your pc should boot fine from whatever drive you specifiy in BIOS. Doesn't matter if there SATA or PATA.

There were no settings to specify the boot order per drive. Like, it just said "Hard drive" in the boot order. I just found a workaround. I have to hit F12 everytime I boot, and select the IDE drive.

did i get it right? you have a sata and ide hdds and windows is installed on the ide hdd... but it won't boot unless you remove the sata hdd. So it means your bios is trying to boot from the sata disk and ignoring the ide. if this is the problem it should be repaired in the bios settings. are there any master/slave jumpers on your hdd's? (i'm not sure if they are still being used.)

Quote from LFSn00b :

And same in english?

Are there any small black/white/blue connector thingies on the back of any of your disks? And if so, are they arranged in a proper Master/Slave/CS fashion (as in, the disk you want to boot from is master, the other is slave). This only goes for IDE disks, though. SATA doesn't use this method anymore AFAIK.

What you checked for probably is what DISK to boot from, but you may want to check what CONTROLLER has priority. It seems to me the PC wants to boot using the SATA controller, but this should be set to IDE controller.
Look for anything that says: Controller Order, or Boot order, or a combination of Controller and Boot and Order

Quote from wheel4hummer :

There were no settings to specify the boot order per drive. Like, it just said "Hard drive" in the boot order. I just found a workaround. I have to hit F12 everytime I boot, and select the IDE drive.

Well, if you can choose what device to boot from with F12, you should also be able to set the boot order in the bios. Just look harder for it, it's probably hidden in some submenu.

Well, before reinstalling windows my computer booted fine. I changed nothing in the bios. I dont understand how re-installing windows can change boot order...

That might be because you changed the partition settings.
Try this;
disable sata
boot up
right click "my computer"
click "Management"
select "disk management"
click on the disk which your windows is installed and right click- "mark partition as active"

i don't know if it is the problem. i might be just spamming.