I've just installed Mandrake 9.2 from a DVD i got with a Linux magazine and after battling it out for it to recognise my USB modem and my new soundcard, i finally started to like it... I've set up LILO for booting but Windows doesn't boot, it tells me command.com cannot be found and asks me to type where it is but whatever i type, it won't find it and gets stuck so i have to manually switch my computer off.
I am not totally bothered by it because i can access my files from Linux but i am a musician and so i have loads of applications on Windows right now - i am trying to find some good ones on Linux and i'm learning to install & use them but obviously, i would like to still be able to use Windows for a little while at least when i need things to get done quickly. I am eventually planning to ditch Windows altogether but would be grand if i could get it to boot to save myself a bit of time right now...
Reformating my Windows partition isn't an option cause most of my applications have been ordered via the internet with a Key code or challenge-response thing and i haven't kept any written record for some of them so reinstalling them would be a big struggle or even impossible and if i can't use them, i don't need my Windows 98.
And by the way, if anyone has any advice about music/Linux, feel free to share it with me as i am struggling a bit. I have installed the ALSA driver for my soundcard (Terratec DMX6 Fire) - i know the digital output doesn't work but i don't mind as i don't use it anyway. I have installed JACK i think but it doesn't seem to get recognised by a drum pattern software i have installed called Hydrogen. And my OSS driver doesn't seem to work so cannot use Hydrogen cause it needs either OSS or JACK driver.

Is Windows installed on the first partition of the primary hard drive? I have a feeling that that's where it likes to be. If it is, I'm afraid I have no idea, and if it isn't then I don't know how to fix it sorry. Have a google. I'm not sure, but I think that GRUB is a better bootloader for dealing with such things.
You could also possibly make a Windows boot floppy.

command.com is usually in C:\

Yeah i know that but it still can't find it! I think there might be an issue with the FAT system but how can i deal with it? Fdisk/mbr doesn't seem to do anything...
And yes it is installed on the primary partition of the hard drive. Windows actually does boot except DOS isn't happy when looking for COMMAND.COM and stops Windows from finishing loading up.
I've done a Google already, fist thing i did actually, but to no avail. All i could find was a page describing this error messgae and saying you should just totally reformat your hard drive - obviously it was a Windows website and they don't even consider you might be running other OS on your computer... Or that maybe you have got legal softwares you actually cannot reinstall yourself.

i had a win98 machine do the exact same thing several years ago. this worked for me. put in a bootdisk and run sys c:. take the disk out and reboot. hope it works for you.
good luck.