Going to post this regardless of JuiceCBean having successfully fixed his issue:
I got tired of trying to figure out which color went to which pin on my cables because they were all different. So, I ended up just building the arduinoboy with a link port built in to the box. Made it much easier as there is reference material regarding the pin out on a link port. With it, I can hook up any old cable to the arduinoboy and even have the option of using a multi-link adapter(DMG-07, after being modded*) so I can hook up three DMGs to the one arduinoboy. Might be useful if you end up modding yours/making a new one in the future.
Edit: Now that I think about it. The reference I used for the link port was the one on the schematic for the arduinoboy.
This whole post, of course, isn't valid if you don't have a dead DMG or two. Seeing as how you can't just go pick up a link port from your local Radioshack. 
*http://www.flickr.com/photos/lameboymusic/sets/72157607419956111/ - Credits to low-gain