I know of a couple of people that suffered from this problem whilst installing Windows 7 so I thought I’d shed a bit of light on the subject.
Basically the cause of this problem is to do with the boot order of your HDDs.
Not that I am 100% certain about this but it seems to be true from my findings, which ever HDD in your system has boot priority over the rest will be the one that ends up with the Master Boot Record, regardless of whether the OS is installed on it or not.
What you need to do when installing is go into the bios and make sure that your system disk is at the top of the list so it is the one that has the MBR installed on it. Understand that it does not matter which HDD you select to install W7 in the installation, the HDD that is first in the boot order will get the MBR.
This is the cause of the “MBR missing” problem that a lot of people get.
Microsoft has a solution to this problem if you did indeed have your boot priority wrong.
http://support.microsoft.com/kb/927392
That would be the quicker way to fix it or you could always reformat, making sure that the HDD you intend to install the OS on is the one that is at the top of the boot priority list.