What are you using to upload? I recommend FileZilla
, and you need to make sure the transfer mode (Transfer->Transfer Type) is set to binary. The other modes can corrupt files.
As I said before, I've only seen 2 other people with this problem; including you, all 3 times have been on different releases. I didn't write the admin code, but when I had Dave look at one of the sites that was having the issue, he couldn't find anything in the code that would cause the problem, and the member switched hosts a couple days later, which apparently fixed it.