Had the same problem and the guidance here pointed me in the correct direction.

My system had been working correctly for a month (Vista Home) and i tried an upgrade to ultimate. This failed and was rolled back.

Then a few days later my system would only boot as per the above - with cd in the drive.

Swapping the boot order on the two hard disks resolved the problem. From the postings and information that I have found this is only a problem for multiple disk machines.

Though I'm not sure how the boot record is moving!