I've read that the keys can be sent via local wireless or infrared, so if it's not detecting, probably isn't an "infrared weirdness issue" (as per your title).
Try having both games take turns to use poketransfer at the transfer lab to receive something from a Gen 4 game.
Apparently if they game thinks the save has hacked elements, that will cause a "no compatible cart" in the other device during the download play segment. Who knows if the keys system have that kind of functionality as well.
Besides that, I can't think of anything