If a system restore doesn't fix it, try this:
from an elevated command prompt type SFC /scannow, (space after SFC) and let the computer finish. If it calls for your Windows CD, insert it. If you don't have one (most retail computers do not) there isn't much you can do. Possibly borrow one from someone (must be the same type as your system, Home or Pro, etc.).
M/Soft has a Windows ISO download site, but you will require a product key to download it. I don't think that a retail manufacturer license key will work. You can burn one of these to a CD and use it to supply a CD for the fix (if necessary). I am not positive this would work since I have never done it, but I have heard of others doing it with success. From how you describe your computer it sounds like you built it so you may have the retail CD already if you purchased a copy of Windows, so the above is not necessary.
In case you aren't sure about an elevated command, here's how: with Windows running, click the START button >Accessories > Right click Command Prompt >Run As Administrator
If all that doesn't help, open the side of the box and check the cable running to the reader, unplug and replug it. If all that doesn't help, most likely the reader went bad.
If you have a retail computer, it may still be under warranty so I would check that out. Same for the card reader itself, if it has an active manufacturer's warranty.
Edited by ranchhand_, 28 February 2016 - 09:23 AM.