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:

sf2-210802-174734.png

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!

@dankcushions said in Unable to configure per-ROM input override for MAME:

point of order, but they do, but it relies on you using the correct physical location or your buttons:

B A R
Y X L

I had not considered this, but this seems very sensible given mame's default inputs (key or retropad event). I had have wired things using the IPAC switch numbers, which won't be hard to change.

1 2 3
4 5 6

EDIT
Here is a post descripting this same problem, which is due to the "simultaneous" core input setting in retroarch:

https://retropie.org.uk/forum/topic/29976/mame-button-mapping-conflicting-with-retroarch-button-mapping

@shadyaw

I would like to know this also!

@Clyde That makes sense - I set up my Pi3 about 18 months ago, so that would have been the last time I really messed around with shaders and options.

@Clyde How did I forget about that? bangs head on desk

Well I feel like a right wally. I applied your code above and it works! However, I must have been mistaken as Yoshi runs awfully with gles2n64 as the emu. I imagine this is why the author blacklisted it. Most of the screen is black, and when you can see elements you only get bits here and there.

God only knows what I was thinking. Apologies to Mitu for taking up your valuable time with this. :-(

Ooops, sorry. Wrong thread.

@mediamogul said in Override Mouse index in Mame2003?:

input_player1_mouse_index = "2"

It works like a charm :)
A big hand to You!

Yep,

Basically i had started out using arcade controls using the Picade Hat wired to arcade controls'
That is recognized by retropie as being a keyboard, later on i set up a FC30 Pro for use with the console systems.

The issue i had was while learning how everything worked i had used different methods on how i was changing settings then i would change something in the a zip.cfg file or the per system retroarch.cfg then get really wonder why it wasn't changing when it was set in one of the overrides that i forgot i had used.

as i say, this time round i am trying to stick to rules as to what i use each type of config for so i know where to look to fix things later.

@freake Stop deleting config files left and right, you could make your system unusable.
What's your system - please answer the questions in https://retropie.org.uk/forum/topic/3/read-this-first.
Use the Runcommand launch menu and enable verbose logging, try to save the config and the paste the error log on a site like pastebin.com.