to continue an old post that the user seemed to have found the solution but never shared it...
I too changed motherboard and wanted to do a repair on my windows install. However, the repair option was not available. i could only install over the current partition or on a new one.
I tried fixmbr, fixboot, etc as suggested by other posts but these are more suitable if your install is screwed up and you cannot boot your install.
My windows installation was fine, I could log in and use it just fine.
I could get into the recovery console - where it actually did find and report my windows install - fine, but when I tried to run bootcfg /rebuild it would fail with some disk/file checking errors that weren't real (chkdsk and low-level surface tests were all ok).
Anyhow, reading that bootcfg /rebuild actually creats a boot.ini file and also reading that this can be done manually from within windows I checked it out and it turned out that in my machine there was no boot.ini.
So, after manually creating one and trying to do a Windows XP repair, I finally managed to get the repair option available.
It seems that windows setup, when reaching the final part of install/repair, is only looking for this file, it doesn't actually scan for actuall windows installs.
I am sure there are many reasons why the repair option would not be available but noone mentioned this one...
Hope this helps someone else.