If you had Windows on 1 drive, left it in the system, and then installed Windows on a 2nd drive while the first drive is still hooked up, this can happen. When you install to a new drive, make sure you take the old drive out first, or at least unhook it.
It's like it does the new installation, however since there is a valid boot file already there on another drive, it just uses it. It's weird, but I have had the same problem. After I did a fresh install on a new drive, and leaving my old drive in with Windows on it, I had to leave the old drive in or Windows would not boot....on my new drive. If I unhooked the old drive, same problem you are having....no boot. So I ended up doing a completely new install again with only 1 drive in the system to finally fix it once and for all.