It seems RPCS3 changed the way they load PS3 Disc games. I use a custom location for my games, so that might be part of the problem...
I found a way to load them though by using a custom path for each disc game. If you create a desktop shortcut in the RPCS3 you get this path: --no-gui "%RPCS3_GAMEID%:BLJM60389"
If you check "Use Custom Command-line Parameters:" with this path in Launchbox, it should boot normally.
NOTE: Installed games (pkg) and disc games installed to hdd0 can be selected normally and booted with the eboot.bin.