Your subject is pretty much correct. When grub (I'm assuming you have grub installed) is not installed into the MBR, the installer marks the boot partition (well, the one where you did install grub) as active because it will not load otherwise.But that should not make your system unbootable, it should load grub.
I think I know why it made my system unbootable. grub wasn't installed to the correct partition. Not my mistake, how am I supposed to know the drive letter of a non-existing partition ?
So what do you want to achieve?
This: install linux install grub/lilo to partition , not MBRcopy first 512 bytes of linux partition to file (linux.bin ) on windows partition
add entry ( C:\linux.bin="Linux") to boot.ini http://www.frihost.com/forums/vt-33598.html But your answer makes complete sense. Thanks for answering.Just one question: in the installer , when I choose install MBR on partition it doesn't show me a list of partitions (WHY GOD WHY?) , instead one has to type the /dev/sdaX of the partition. How can I know the /dev/sdaX address of the / partition of debian?