I updated the core and it still doesn't work. Nestopia and AdvMame all work great for me with no calibration/tweaking needed. Just plug and play. Nothing works on Genesis Plus for me, re: light guns.

@mitu Life saver! I did a RetroPie update through install script (to update all packages). That fixed my problem.

@quicksilver I have 6 button setup working on both emulators as of now. I found the settings you mentioned in Mortal Kombat II but changing them made no difference. I went over everything on my setup and was stumped. I booted up a fresh image, completely up to date, configured my SNES and Xbox controllers and put on my Sega games only. I made the changes to the respective config files and presto it works. After changing the setting you pointed out that I missed earlier in Mortal Kombat. I don't know why my original setup was not working. It has to be something I modified but I haven't found it. Thanks for you help and if I track it down I'll let you know. Update: I think I found the problem. When I updated in the morning I did both binary and source, I've never used source before. It wrecked my controller configurations. It had my generic SNES listed as generic and just SNES, and the Xbox controllers were listed as generic Xbox, the original config, and Xbox 360 Pro. Every game I launched listed the two controllers I had connected twice and then worked in piece. Not sure why updating from source would do this as I have updated from binary and it was fine. In the future I will probably unplug all controllers and use the keyboard for updating.

@cjax08 from what I have found: iso is larger than bin bin is larger than chd and chd is smaller than pbp format for a psx game though not by much

I think the good way id to create 2 core option files and launch the game with correct option file depending u want to launch in jap 60hz or use 60 hz or pal 50 hz. Is possible in gamelist to set the lauching command specifically for each game?

Ok then you are gold... I can't help you with the reading...there might be a way to use a smaller font...but just wait a few seconds and let it scroll and read what it says. Look what I posted above... After that has been set...go back to the "quick start" menu and then go to save game configuration file....then resume and quit the game then restart it to see if the settings stuck. You can do a quick test by enabling the 4-player device and then backing out and choosing reset then resume..this resets the game and it will see that has been changed. But you have to save the configuration file for it to stick...unless you want to have to enable it every time you want to use it :P

For anyone interested, I was able to figure this out, I was using crt-pi shader, but for whatever reason this causes problems with genesis plus gx. Using crt-pi-vertical shader produces the identical results that I get in other emus using crt-pi shader.