I fixed my problem with the gameboy roms and now I'm ultimately happier. There is no support for people who use linux on their home computers and have modded xboxes, so I had to figure this out on my own. I hope other people who were in the same situation can google "xbox linux" and find out how to successfully ftp binary files onto your xbox. First of all, I have to use the regular console ftp client that comes with slackware. I am able to transfer data back and forth with it, but I didn't know that it defaults to ASCII as the default transfer method. You have to use the binary command after connected to the xbox to change the tranfer type to binary. I came to this conclusion because I knew that more than just gba roms were having problems with being transferred to the xbox. Several video files (.avi, .mpg, etc) were not playing in XBMC, either, however they would play if I burned them to a cd and played from there. GBA roms were playing if I had them on cd and copied them to a directory, too. I experimented with transferring roms that already worked on my xbox (roms that were put on by a friend who uses windows) to my computer and then transferring them back. They didn't work after being transferred back. That is how I figured out that I needed to change the transfer type to binary. So, now I can transfer to the xbox successfully whatever I'd like, just so long as the ftp client is set to binary transfers.
Almost as soon as I figured this out, I discovered another console ftp client called ncftp, but I didn't think I could ftp into my xbox with it at first, because it always gave me an error message upon typing ncftp xbox (the network address for the xbox is set in my hosts file in /etc). ncftp worked when I did ncftp -u username -p password, and once I was connected it was better for ftping into xbox w/ linux than regular the regular ftp client %100.
Differences: With regular `ftp`, you can only transfer files that are in the same local directory that you were in before you ran ftp. Example: If I'm in /home/anithen and ftp into the xbox with expectations of typing "put /home/anithen/roms/romtitle" and succesfully getting it transferred it will fail (with ftp and ncftp, I cd into the place where I want the stuff I "put" to be rather than specify it, so "put game path\to\game" would be wrong, but "put game" would be right, just transferring the game into your active remote directory. With `ncftp` you can put files that are in directories other than the active local directory (the directory you were in before you ran ncftp), so you could've cd into a directory called roms on your xbox with ncftp, and then typed `put ~/games/sf*` to transfer everything that begins with sf to the active remote (xbox) directory. With ncftp auto complete works with xbox directory names and filenames, too. That is not the case with regular ftp. With ncftp it will ask you if you want the username and password to be saved the xbox, too, so in my case I can just type "ncftp xbox" to get into the xbox. Ncftp goes further with a bookmark feature, too, that saves the last active xbox directory you were in, so that's just added convenience. Ncftp also transfers date in binary by default, so stuff you transfer to the xbox will work automatically if the transfer is successful.