When you say "upload", do you mean, from the camera to the computer?
Do the damaged pictures show up fine when viewing on the LCD of the camera?
You may want to try a USB card reader and see if that makes any difference. In the future, you may want to try formatting the card in the camera after you're copied the pictures off. Generally, you shouldn't need to do that, but if the camera has been disconnected from the computer when it was trying to copy some data, it can cause corruption on the card which can result in damaged photos, and that corruption can be cleaned up by formatting.
It goes without saying that formatting will erase what's on their now (though it usually can be recovered with the proper software), so make sure you're got everything off beforehand.
There have been a few deals recently for a Kingston 2g card and a USB reader for under $20, and you can find stand-alone readers for even cheaper - I got one free after rebate, and it was only $7 before.