I think the problem is that title launcher runs them in a way that doesn't bypass signature checks even if you are on a CFW with patched sig checks. How we would go about fixing that, I have no idea. HANS seems to be running them just fine though, and the source code for that is available, so maybe someone could take a look at that and see what HANS does that title launcher doesn't.
My legit .cias start up properly from title launcher (Pokémon, MK7, Mario 3D Land, NSMB2), it's just the ones with invalid signatures that won't.
At least I can still select them with svdt to backup/restore save files

which is the only thing I use homebrew launcher for anymore, really. I just start up games straight from the home menu.