while you wait for a better reply,,,,I don't know about sys commander but assume its in your MBR.
2) so maybe you need to look at the chainloading of grub via the ntloader way mentioned here
http://www.linuxquestions.org/questi...troubleshooter
3) its early days yet, but maybe if you look at how grub works you might consider putting grub in mbr to chainload 2000 and direct boot linux?