D
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I decided to check and see something. Sadly, I figured out why. I have an EZ 3-in-1 in my slot two. With it in, I get linking. But when it's not in, I get no linkage. Nothing about migrating. So it appears the GBA link feature isn't a true link. It appears to copy the GBA game to the slot 2 and alter some of the code to the DS game to see the GBA game. So it's not a linking like we were assuming it to be.
Ah, well at least that solves it then. Thanks