You had the problem with lilo boot.
You have to set the lilo parameters right and write to right drive.
As you told, you have windows in first drive, assumed /dev/hda,
and linux in second, /dev/hdb. You need to go in linuxconf and write
lilo in the second drive, /dev/hdb. I had also problems when
I have great problem with Xfree86 configuration to SiS530, I can set it
in X-windows only with generic 640x480x8bit. I ghanged to SiS530 with
800x600x16bit in DrakConf, it seems ok and after saving configuration
and starting X again, the old configuration comes back. The XFree
package includes
