Generally it has always been the case that you do not want to erase or format a cameras SD/CF card on WIndows, always let the camera do it.
However I have never seen this happen
Which camera/model was it? Though the formatting is probably still FAT32, there are parameters (like cluster sizes) that other OSes (linux) can set and use that windows will have problems with. Course if that's the case that's petty poor testing on the manufacturer's part. But also, maybe it's actually the card readers fault. Have you tried it in an external USB reader? (Or a different one)
I think you found your one solution (and really it's something I always do having taken thousands and thousands of photos on a dozen digital cameras over the years) ALWAYS copy the data to a safe place before doing ANYTHING