How did you repartition? Most probably, your windows partition has changed number, eg hda1 became hda2 or somesuch, which would invalidate the boot.ini file. I believe the easiest fix would be to use the windows recovery console (google for it and the fixmbr/fixboot commands).

Beware, though, that fixmbr overwrites lilo in the MBR - which you might have to re-install in order to dual-boot, or edit boot.ini to add a linux entry from the windows boot loader. If you created another primary partition for linux, another option would be to install lilo there, make that partition active/bootable and leave the windows boot loader alone in its partition...