I might be wrong about this, but apparently the 7800 emulator is an older version (2008?!) and has pretty spotty compatibility compared to the 2600 side of things.
Way off topic, but are there any good paddle options for emulation on a PC, Pi, or console? I'd like to check out a few arcade and SMS paddle games but have never really looked into it. I seriously debated on buying the Gamestation just for its built-in paddle dial, then saw it won't work with added games, won't work on a PC, and doesn't even work too hot with the included games. I've heard good things about the VCS classic controller but didn't know about its compatibility with other systems or emulators.