Thank you everyone for your feedback and suggestions! I think I figured out what is causing the conflicts I am experiencing, for which I'll reference the following screenshot of the mame input configuration for sf2.zip:
My rebindings are attempting to "relocate" buttons, assigning buttons 1->2, 2->3, 3->6, etc... (as noted before). The end result is that only the RetroPad bindings changed, not the keyboard key bindings. The OR clause in the mame mappings thus maps one key/button to two events and that ends up breaking things!
For completeness, I've done some more work...
I checked fuse.rmp, it did not have the "-1" settings applied to anything.
Each game remap would have been created from the fuse.rmp (using the retroarch menus.)
I then checked all my game remap files. 13 of 28 files had this problem.
Next I tried to recreate using the retroarch controls menu.
Cycling right through the available options that can be mapped to the port 1 controls I have:
Then back to "---"
The (1) etc are my addition, "Fire" appears 3 times, "up" twice.
I set some buttons to each of these values, wrote a game remap file and checked for "-1". None of these options generated the "-1".
Next I cleared the options on buttons A, L, L2, R, R2 & X (all originally set to differently) and bingo, I recreated the problem :
There appears to be a bug. When clearing a mapping using the retroarch "Controls/ port X Controls" menu from any value to "---" the resulting remap file contains "-1" for that key and this stops you mapping the button using the Retroarch "Options" menu.
Plug in a Keyboard
While in Emulation Station press F4 to open the Terminal
sudo nano /etc/modprobe.d/xpad.conf
Change xpad triggers_to_buttons=1 to xpad triggers_to_buttons=0
Accept the changes.
Return back to Emulation Station by typing
(In my case, I noticed that the X-box controller had started acting strangely while in Emulation Station.
The D-pad buttons swapped positions in Emulation Station as they were previously in PPSSPP.)
Remap the controller in Emulation Station.
Remap the controller in PPSSPP if necessary.
(In my case, this was not needed.)
I'm not sure why this issue is affecting some people and not others.
Apparently, the problem is caused by the Trigger buttons somehow.
I will guess that you must be using the latest retropie, and since the way reicast now handles joysticks, the reicast-joyconfig method commonly found on youtube that everyone is trying, no longer works. The docs need updating, but here is where I found the solution for my similar problem after first installing retropie on my pi3b+:
I think that thread should be stickied until the documentation is updated. Note that the bottom line for me was the reicast autoconfig (which uses es joypads) chose the wrong device id#'s in emu.cfg. The reicast-joyconfig did what it was supposed to for my 4 controllers, and created working evdev device files in reicast/mappings/. So all I had to do was change the bottom[input] part so the "players" lined up with the right "device id's". In my case I had keyboard=0, mouse=1, joyou dual arcade=2, joyou dual arcade=3, and xbox one s=4. I initially -1'd the keyboard and mouse, and had 3 players configured, but that didn't work at first (+start reicast wouldn't respond). I went back to emu.cfg and -1'd my player 3 (the second half of the joyou), and reicast responded fine showing both player controls... and games also worked 2 player. I haven't gone back and tested re-enabling player 3, but I wonder if having the dual arcade device may not work out with that.
So bottom line, if you ran the joystick config script, you probably already know which device id #'s need a player # to go with them in emu.config [input] section (the rest get -1'd out). More than likely the proper working evdev files are already in your mappings folder, so after getting your 0 and 1 behind the proper = sign in emu.config you should be good to go.