Ok so I just finished modding a friend of mine's xbox and installing a 400gb hard drive. For the most part it went smoothly, a few minor headache's but I got it done. Anyways, I got it all set up and everything was working perfectly, But then I went to put some homebrew programs on and I ftp'd them over, rebooted it and they weren't there. after trying everything I could think of, reinstalling them. rewriting the evox.ini countless times. I can't get the programs to show up on the xbox.

Any ideas?

First of all, are you using F+G, or, if you are using only F, did you format it with xboxpartitioner/32kb clusters?
Make sure the homebrew .xbe's are named default.xbe