In camera formating is not necessarily low level formatting, it merely marks the card as empty in the Fat Table.
Windows has two format options, quick and full. The quick is basically the same as in-camera formatting, while the full format is more thourough.
If there is a issue, do a low level or full format. The 5D MK III has a option to do a low level format on a SD card which should fix a damaged card as well. I'm not sure about other Canon models.
I use image rescue 4 to erase and repair a damaged card. It takes several minutes to totally erase a card. After erasing it, I format it in camera.