I never had problems with starting smash:
Bought cartridge - backup rom on gateway 3ds - or converted to .cia
all 3 methods starts on my o3ds(S9.2/E10.3) AND on my n3ds(S9.0/E9.5+newest NVER and TIGER) (doesn't matter gw mode or rxmode).
Since a certain update (maybe 1.08?), only starts when both on emunand.
What I'm more wondering about is why my save in the cartridge seems to be ok on o3ds but not existent on other 3ds?! I had to backup cartridge on my o3ds (where I initially used the cartridge), then restore the same data on the same cartridge but on my n3ds. Worked. But why?