My advice to not use Mame for NES and SNES or any other console unless it does not have a better emulator option available.
NES and SNES has several other options which are much better. NES has the stand alone versions of FCEUX, Nestopia, puNES and Mesen plus the Retroarch cores FCEUM, Nestopia and Mesen. Mesen is extremely good, near 100% cycle accurate now.
For the SNES you have stand alone versions of Snes9x, BSnes and Higan along with Retroarch cores for each. All of them are superior emulators compared to Mames emulation of those systems.
It certainly is strange though that some games work and others don't when launching through Launchbox but work fine when going through Mame on it's own. I do have some consoles running through Mame and they work fine but I only use it for Colecovision, Intellivision and occasionally Atari 5200 and FM Towns Marty.
Edit:
Bizhawk is another great option for NES and SNES emulation.