Is my install of Windows corrupt?

My computer was working just fine but I decided that I wanted to install an OS on a secondary hdd (to put into a different computer). I disconnected the sata cables from my hdds and then hooked up the other hdd. I don't remember if I tried turning on the computer with the sata cable disconnected but the power cable still connected, but I didn't think that that would cause me any issues. Now, after reconnecting everything back to the way that I had it, my original boot drive doesn't want to boot. The secondary drive which has Pepermint Linux on it still boots up just fine (I never did install Windows on it like I was planning to) so I am using that OS to be able to use my computer. 

Now, when I turn on my computer, I see the mobo splash and can access the bios (the boot order is correct) and then after the splash goes, it goes to a black screen with a flashing underscore on the left side of the screen. Id my install of windows corrupt? How can I fix it? 


EDIT: I can still access the files on the non-working boot hdd via Pepermint, so the hdd itself seems to be working. 

Did you check if your IDE/AHCI settings match? :)

Still set to AHCI just as it always has been. 

I think windows has put the 'MBR' or whatever header it needs to boot on ANOTHER drive that you were installing to.

Sounds crazy right? Well, I had that sh** happening alot to me.

Were you installing with serveral HDDs connected?

Do you still have both HDD's connected or just your original Windows Drive?

Well, in any case, if i'm right, use the windows recovery cd so he can clean up his own mess with the automatic repair thingy (If you have Windows 7 or 8), provided that you have put the hdds in place that you will keep using.

I don't think that I was, and I never got around to actually trying to install windows on that secondary drive anyway. But now that I am looking at my hdds (they are all connected now) via Pepermint, I see a bootsect.bak file and a boot folder on one of my storage drives. Could this have anything to do with what you are talking about? I have had all of my hdds connected while trying to boot, so I would imagine that it should work just like it had been in the past. 

I tried with all of the hdds that were connected in the past as well as just the boot hdd. I am now using just the spare hdd with Pepermint on it though, if that is what you are asking. 

I second this...

Should I do a repair install with only the boot hdd attached? I don't want necessary files getting spread out over my storage drives. 

might as well

I'd suggest you to pull out any unnecessary usb sticks and HDD's out just to be safe..

Also, a windows DVD would be a bit safer than a USB stick because I've had some bad experience with it (especially with windows 8). Good luck budy!

Yeah, I did both of those things. I decided that a fresh install wouldn't be a horrible idea (I like fresh installs anyway).