Can you boot from your windows CD? If you were reformatting you'd either need to do that or get a
bootdisk that you can use...obviously you'll need an environment you could boot into in which you could access the drives before your can reinstall so there's no point in reformatting until then.
You might want to try some weird things, like switching around IDE channels, unplugging one of the drives, etc before you go to the trouble of reformatting though. I take it that when you say you recently reinstalled windows you mean that you installed over top of an existing copy of windows? Why did you do that (just curious if it could have anything to do with what's going on just now). Also, what do you mean that windows can't detect the drives exactly. Are they not present in device manager, or do you just not see them under my computer?