I am having the same issue, Launchbox shows all cores as missing. When I try to run a game associated with Retroarch, nothing happens. I can run the game just fine if I start up Retroarch directly and then run the game. Also in Launchbox I cannot even select Launch with... or Configure... on the games associated with Retroarch. Greatly appreciate any help.
Edit: I found another post from another person that posted the solution. I had to add Game Boy on the associated platform list by clicking the very bottom box. I was looking for a +Add platform or something, not very intuitive like this but got it working.