Which setup program are you referring to? I'm not too clear on whether you're trying to fix things from Windows or from Linux
Lilo should easily be able to make your drive bootable again. If you can boot up using a floppy or some such, or (even better) a Linux CD that gives you the option to go into maintenance mode, you can mount your Linux drive and get at your /etc/lilo.conf, and run LILO again to fix the MBR. I wouldn't trust any Windows utility to fix an MBR. I recently had a problem with my Windows boot record (on the C: drive, not on the MBR), and Windows couldn't even fix that properly!
As long as you can get to your bootable image (/boot/vmlinuz or whatever it's called; it should be listed in lilo.conf), you should be able to fix it!