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It would be very helpful if you could get to your /etc/lilo.conf file and post it here.
More than likely it is not an MBR install problem, but rather a problem with how lilo is configured.
You didn't state which version of Windoze you have on your primary hard drive, but if it's WinXP or W2K, you could use either ntldr with Lilo boot code on the boot sector of your Linux space or you could install lilo with its boot code on the MBR of your primary. If you have Win98/98SE, then you must use Lilo on the primary MBR, or boot Linux from a diskette, or use some third party boot manager.
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