I did some research and it seems to be a hardware issue with this motherboard (and some other Intel Atom based desktops). They are designed for Laptops with built in monitor panels and it defaults to that during boot, and of course as it doesn't have one I can't see the login screen.
I added "video=LVDS-1:d video=VGA-1:e" to my grub configuration and I can now login properly. Even though I guess it's a workaround more than a fix I guess this bug can be closed as it's a hardware bug and not really a debian bug?
