Now that that is over, I bring great news!!!!!! Me and Darth (96% Darth actually:p) have solved the problem of secret bases in Ruby. I have a completely running copy with 256 OWs and fully functional secret bases sitting on my desktop right now!!:D As soon as I port it over to Emerald, I will edit the tutorial to teach you how to fix it!
Edit: I finished porting the routine today. I haven't had a chance test it, but once it is confirmed, I will update this tutorial.