before re-installing windows, try booting from the windows CD, you should be able to boot to a text mode recovery console, (note this is not a repair install, it's an option before you get to this).
from here the CD should be able to scan the hard drive, and use the fixboot command to fix your boot sector...
thevil1's drawing wasn't exactly accurate... (but I see why that conclusion has been drawn).
what happens is that when windows is installed it points the boot sector towards the windows boot loader...
so your disk looks like this.
|boot sector||partition 1 (with windows installed)||free space|
the boot sector says, go to partition 1, here you find the necessary files to boot the machine into windows. since there is only 1 windows installation your boot loader says load windows that's on partition 1...
if you have 2 copies of windows, your windows boot loader recognises this, so the boot sector says, find the boot loader on this partition (say partition 1).
the boot loader then lets you choose between windows installed on partition 1, or windows installed on partition 2. (with a simple black/white text menu).
When you install windows it does not recognise Linux installations, so if you have a linux machine and try to put windows on it to duel boot, you soon find that the boot sector on the disk has changed to instead of look at your /boot partition that has the linux boot loader (grub/lilo etc) on it, it just looks at the window one, and so only finds windows installations.
for this reason when you want to set up a duel boot machine it's always easiest to install windows first, then linux.
because when you install linux, it does recognise that there is an existing windows installation, and it adds this boot option to it's boot loader giving you the opportunity to dual boot.
you disk now might look like this...
|boot sector||partition 1 (with windows installed||partition 2 (with Linux installed)||parttion 3, (SWAP)||Partition 4 (boot -with grub/lilo installed)|
the boot sector on the disk now has the instruction to find the boot loader at partition 4, so looks there for a boot loader.
this boot loader then starts and gives you the options to load windows or Linux,
now that you've removed linux there is no partition 4, your disk is back looking like this
|boot sector||partition1||free space|
but your boot sector is still trying to find partition 4, (rather it's looking for the sector of the disk where the boot loader has been installed).
you see, the problem isn't that Linux has "wrapped" it's self around windows, and by deleting Linux you've deleted windows.
the problem is, (or at least was at first) that the boot sector was looking at the wrong place for a boot loader...
(when you installed windows it was told to look at sector 0x12, when you installed linux is said, look at sector 0xf1 (for example), all you need to do is Change the boot sector to tell it to look in the right place again, (0x12))...
as I said, there is a handy utility for doing this on the windows CD in the text based recovery mode,
fixboot.