It looks to me that your data somehow got corrupted on your sd card. Do you reformat your card after each upload to the computer, as this clears up any bugs that might do this at a later date. My suggestion would be to get an external card reader as this is the only way you can do it, and also download an sd file recovery program off the internet... I'm unsure if you are using a mac or windows so I can't advise you on which program to look into. I am guessing you use windows though and I use mac so I don't have any experience with their programs, but I'd give this one a shot.
Good luck with that man, I've been in your position before, but much worse because half of my photos weren't appearing and the rest were merged into multiple pictures.