Boot Manager missing when no disc in disc drive

So I have an bit of an odd and I think unique problem (as many searches came up with no solutions). Simply put, my boot manager is missing, but only when my windows install disc is not in the disc drive. It started several months ago and I just left it be, let the disc it int he disc drive and it was not that big of a deal. But just did a clean install couple days ago I re-installed windows 7 ultimate 64-bit on my computer (using an upgrade disc if that makes a difference). I formatted the drive with what I guess is a quick format (the option the install disc gives you). I have tried doing a repair with the install disc but no problems are found every time I try.

Anyone got any ideas how to fix this problem? Or I guess another way to ask, how do I get the computer to look for the boot manager on the hard drive and not in the disc drive?

EDIT: Also sorry if this is in the wrong section, I didn't really see a section that fit this problem, but if there is a better section for it, could a moderator please move it.