I had it set to transfer in ASCII mode, but I looked carefully and noticed that it was opening the directories in ASCII mode, but transfering in binary.
So I downloaded cuteftp to use instead. I set it to ASCII and it did the same thing. For some reason, the programs think these files are binary.
So I overrode the settings and cute ftp asked me if I really wanted to upload these binary files as ASCII. I said yes.
I re-uploaded just about every single file, but debug.pl still thinks most of them weren't uploaded in ASCII mode.
I've uploaded one directory five times, in ASCII every time, and debug.pl is still spitting out all the files.