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LILO does not work with NTFS very well, and is a somewhat older version, grub should work very well. But during install, you should have opted for manual partition, and set it up manually. Or you can use a third party booting program such as boot magic, that is what I use and have no problems. You can use lilo as your linux booting prog and install lilo to root. that way you don't mess with windows whatsoever. Boot magic tells your computer which way to look when it boots. I highly recommend it.
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