So I recently had to re-install Windows 7. All is working fine except for my HDD. I have an SSD (with OS and main games) and my HDD (for other games and pictures/movies etc.). So, I noticed that I couldn't use or download anything to my HDD. I tried to format it, but when I click format it just says, "Windows cannot format the system partition on this disk".
Ok so what's happened here is that windows has installed on your ssd but chosen your 1tb drive to put the boot manager and whatnot on.
You should be able to shut the system down and disconnect the 1tb drive.
Then boot from your windows disk or usb key. Select a language, click next, then click repair your computer. It will search for a windows install to repair, don't worry about what drive letter it finds.
Select that install and click next.
Now click on command prompt.
Type in bootrec.exe
Type /FixMbr
Type /FixBoot
Type exit.
Click restart, and hopefully it should boot from the ssd normally, pop the disk/usb stick to be sure.
Once that's done you should be able to reconnect the 1tb drive and format it.