I've noticed the same with the GBA I did myself. I don't see it on the GBA I got pre-modded, but I definitely know what you are talking about. I think you'll have to adjust the small pot they mention in the guides, but I'd wait for confirmation from someone here. Wiggy probably knows what's causing this.
Oh good to know there is probably a fix. It's a wiggy mod that I bought, and I did email him today about it. So I'll patiently wait for a reply before I go muck it up on my own.