you might have a bad/corrupt boot sector on your harddrive. Your Windows cd has it's own boot sector and when you don't hit a key to boot to the CD, it checks your hard drive for an OS and runs it. The easiest way to fix it (if this is the actual problem.. just a educated guess this far) would be to re-wrote the HD's boot sector. You'll need to boot into DOS and run the command "fdisk /mbr" (all it does is re-write the Master Boot Record and partitions, which includes the boot sector)
Notice i said DOS.. i don't believe this is something that can be done via the recovery console. If you don't have a dos boot disk, you can go to and download one. I would suppose most of the DOS disk images would include the FDISK program.

