> I don't know if its just my screwed up system or debian, but this has
> happened twice now.
> Installed debian once with the w32 installer and once with the normal
> installer. Both times I chose not to install the MBR. Upon rebooting I
> found my system unbootable. To fix it I had to boot with hiren's and mark
> my windows system partition as active, after which it happily booted into
> Wat is happening?
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. If you mark the Windows partition active, then you will not be able to boot into Debian. So what do you want to achieve?