I don't know exactly what the software you ran does, but if it modifies the boot sector of your windows partition in anyway, you might have to either reconfigure LILO or install the latest version. Also, note that some things like hibernating your computer can make rebooting IMPOSSIBLE without wiping lilo off your boot sector and using a regular windows bootloader. There are some other things that one can do to one's boot sector that LILO doesn't have a clue what to do with them, (Trust me, I've done a few of them) but those are usually the result of some very stupid things when installing and configuring Windows. Just some thoughts. Does windoctor have a) a restore to previous settings feature and b) a command line interface, if yes to both, boot using a windows boot disk and run windoctor again and restore to previous settings. If not, try running the 'lilo' command to reinstall lilo, ya never know.
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