@substring Ok. I was hoping it was a common thing, like I had to set something special up in MAME. I will check my roms and see if maybe they are not the right ones for the new emulator?
I have no other controllers plugged in. I will plug in a keyboard and see if that works. I just wanted to ask here fist in case it was a known and simple fix. 
Is it possible when I copied the /roms folder from the old system, that some MAME settings in there overwrote some new ones?
@substring Does not work at ALL. I guess it could be that the ROMS are not working (my first thought), but then I noticed that they were all not working the same way (appear to be frozen), then I figured it must just be the GPIO not working. I have to reset the Pi to get out of mame. Hotkey also does not work. As if the GPIO is off when on mame.
So, I just did a fresh install to 4.1. I backed up my /roms folder and then moved it back to the new install (if that is important). But now MAME roms don't seem to work... Or at least the GPIO does not seem to work, but ONLY in MAME.
Any idea where I should start problem solving?
Dang. But thank you all for the responses. At least I know I HAVE to reinstall.
@oyyodams I get:
++ python /usr/lib/python2.7/site-packages/configgen/settings/recalboxSettings.p yc -command load -key updates.type
I see "type" is missing, but it shows right on my .config file:
updates.enabled=1
wifi.enabled=0
audio.bgmusic=1
audio.device=jack
audio.volume=100
controllers.gpio.enabled=1
system.hostname=Game_Table
wifi.key=mysiswill2
wifi.ssid=mine2
kodi.atstartup=0
kodi.enabled=1
kodi.xbutton=0
update.type=stable
@subs Yea, I think that worked. Thank you. It seems as if you do NOT have to map both Joystick 1 and 2. It seems (so far) to be ok with using joystick 1 for player 2 also. At least in MAME and that is all I was looking for anyway.
Thanks for sticking with me. I think I expected it to be complicated and you expected it to be easy. You were correct. Now I just need to buy ONE more button and drill another hole.
Thank you.
Ok, so I need to install ONE more button and map that new button to the P2 Start button and that will act as "choose 2 player" and then the ONE PLAYER joystick and all of it's buttons will work for player 2 automatically? So the ONLY button that needs to be set up for 2 player (one right after the other) is the P2 START button? Then when it is P2 turn, the joystick and buttons will work for player 2?
@subs Yes, I guessed that I do indeed need to map a P2 button. That much I had figured on my own. I came here to see if anybody knew how I would go about doing this. I am guessing that some people must have a working P2 button on their machine. So I am just inquiring about how they went about this process.
Ok, but when a start a game on MAME, it says "Press 1P or 2P". When I set up the controller (in recalbox) the button I choose as "start" ends up being the "1P" button and the "Select" button ends up being the "add credit" button. So how do I select "2P"? I don;t have or know how to assign a button so that Mame recognizes it as "2P" button.
I am sure this is covered somewhere, but I can't find it. I have a cabinet that I have had for over a year now, but I would like to be able to make it TWO player, while sharing the one GPIO controller setup. I assume I need to somehow set it up to share the controller but I will also need a button for "two player". (It is a retro machine and I really just do MAME type games on it... Pacman, DonkeyKong and so on). I have it set up now so the "Start" button chooses "one player" and the "select" button "adds credits". Do I need to add another button for a "two player" button? And then how would the system know that was the "two player" button?