What i did was set up all my partitions that i will be needing first! that includes all the linux partitions and the windoze partitions using fdisk.
allowing for the linux partition to be the boot partition because linux knows what it is doing.
then have lilo as your boot loader
Code:
Disk /dev/hda: 255 heads, 63 sectors, 4866 cylinders
Units = cylinders of 16065 * 512 bytes
Device Boot Start End Blocks Id System
/dev/hda1 * 1 6 48163+ 83 Linux
/dev/hda2 7 1530 12241530 5 Extended
/dev/hda3 1531 2167 5116702+ 7 HPFS/NTFS
/dev/hda4 2168 4866 21679717+ 7 HPFS/NTFS
/dev/hda5 7 771 6144831 83 Linux
/dev/hda6 772 1275 4048348+ 83 Linux
/dev/hda7 1276 1429 1236973+ 82 Linux swap
/dev/hda8 1430 1493 514048+ 83 Linux
/dev/hda9 1494 1530 297171 83 Linux
and thats my partition table works fine, the good thing about manually setting up all your partitions is that then you know how it all fits together and if something does go wrong you have a head start in fixing it