I'd stop using that card reader immediately, and the same goes for any card that won't format in the camera. The card reader is possibly defective, especially if it worked right before but now doesn't. If it worked right before, but it's not working on a new system, try going to the card reader manufacturers site and looking for a firmware upgrade for the card reader. They're rare these days, but they do exist. Most just don't need to upgrade the firmware, USB 2.0 has been mastered years ago.
The most accepted and I think reliable practice is to always format your cards in the camera and not the computer. Period. And then to use a card reader and not the camera to download the images to your computer.
Most of us have umpteen card readers.. one in every bag, attached to every computer, etc.. In Thailand good fast card readers (actual well made 5-1 or better card readers) could be routinely found even in super markets for the equivalent of $2-$3.. but for some reason here they're often 10x that. In any case, next time this happens try a new card reader first and don't keep sticking different cards in a suspected defective card reader.
I was hoping we'd be seeing USB3.0 card readers by now but they're not yet common and they're very pricey. If you have a desktop or even a laptop with an esata port look at this SATA CF Card Reader from Lian-li
. It works well and is very fast compared to USB2 readers. Well made and inexpensive. I paid $33 for mine on Amazon a while back, I'll bet they're cheaper now. And that was with a high quality brushed aluminum 5 1/4 to 3.5" adapter and cables to use it externally with USB 2.0 or esata.
Good luck solving your issue.. I'm sure it just involves tossing the defective cards and reader and replacing them. A hard pill to swallow, but necessary.