I recently upgraded both my mobo, cpu and ram. The new mobo and cpu are 64-bit. When I try to boot into my old hard drive, it does not see any operating system and wants to load cd/dvd.

I had previously used a 64-bit Windows 7 install disk to install windows with my old cpu, which I seemed to work with it.

when I use the same install disk on a blank hard drive, I can easily install and boot into this clean copy of Windows 7.

I can also see the contents of my hard drive from this new install, and cannot see any issues with system files missing or anything.

Any tips as to what I should do? I am planning on swapping out my new mobo and cpu for my older one which they replaced tomorrow, but I just wanted a bit of advice to see if there was anything else I could try.

A change of motherboard means a change in hardware. You will need to reinstall windows!

Any way I can reinstall without losing all my programs?

Backup everything you can, but unless you have the installers for your programs...