I was having a rather odd problem with my display recently. My motherboard has onboard video, but I was using a separate nVidia card as my primary display. The video card has an HDMI port and a DisplayPort. I had monitor hooked up via a DisplayPort to mini DisplayPort cable with the DisplayPort hooked up to the video card and the mini DisplayPort hooked up to my monitor.
I was booting into an Ubuntu install, and the problem was that I was getting no display signal at all before X came up. This is a problem, because the hard drive needs a decryption password and I couldn't see when it was asking for the password. I thought it might be an issue of the system getting confused over what the primary video was, as it worked when I plugged into the onboard DisplayPort, and also worked when I plugged into the HDMI port on the nVidia card.
This was a workaround but was annoying as it meant having to swap cables around every time rebooted. Finally I tried replacing the DisplayPort to mini DisplayPort cable I was using to one that had full sized ports on both ends and hooking up into a full-sized DisplayPort on my monitor. This for whatever reason fixed everything, and now the graphics on boot work fine.
I am stumped as to why though. Was using the same exact output port on my PC, tried using two different DisplayPort to mini DisplayPort cables, and two different monitors, got the same effect. Can anyone explain this?