@stoney66 well - switched the roms and now they work. Centipede, Missile Command, Golden Tee 2 are all working now under AdvMame. Marble Madness is still unhappy, but I would assume that's still just a rom issue. I think this issue is likely resolved now. Thank you everyone for your help! @mahoneyt944 and @stoney66
Thanks! This gets stranger.
Originally I was using a MicroSD Adapter to read the card on a built-in SD card reader in an HP Elitebook 2540P I5 laptop running Windows 10. Today, I used a different micro SD card reader (a USB version this time "T-flash USB") - didn't even know I had one, but found it by chance when I was going through my USB drives in order to install gpartLIVE as bootable drive) on the same laptop. When I looked at the micro SD card using this USB reader, disk manager showed the 256MB partition, another space of several gigs, and a large unallocated space (albeit TOO large). I wiped out the partitions (using Diskpart I believe). Then I saw a capacity of 2TB of unallocated space (on a 128GB card!!!). I got gpart to run on my other Retropie SD Card (never actually needed the USB drive) and using the same USB reader, it too reported 2TB for total capacity. Other Linux utilites reported the same capacity. I tried a different SD card in this USB reader and that reader always shows SIZE 2TB, but it does show the correct partition sizes. Now I had the opposite issue - too much space reported. Various partitioning and formating utilities choked b/c I think they were trying to read/write beyond the actual capacity of the drive. On a whim, I put the card back in the original Micro SD card adapter and disk manager showed 116GB unallocated. I created a simple volume and it worked. I imaged the card and the Pi booted. Almost 24 hours later and I'm almost back to where I started. I thought these adapters were just devices which passed the connection through pin for pin with no 'smarts' in-between. Maybe the built-in card reader had an issue? Dunno. In any case, thanks for all of your help.
@Kartman Hello, I cannot find a good scanline reproduction with ADVMame. It does not use shaders, only overlays. Tried to make a few scanline overlays and had no luck. There are video options for scanlines, but I could not find anything that looked as good as shaders do.
I decided to update my question, just in case someone comes back to look at this asking the same question I was.
I'm using joystick encoders instead of a keyboard encoder. What I found is that retroarch allows you to setup a mouse for use with the game. So my trackball goes in as mouse 1. Since I do not have a UI running on my setup, I don't actually need mouse buttons. I only need the trackball input for the games.
What all this means is that the retroarch setup will use a joystick along side the trackball... meaning the buttons going through the joystick controller work along side the track ball and I don't need extra buttong for left and right mouse clicks.
@whoremoan I believe your post describes an issue I have also been struggling with for some time, but recently made some headway in diagnosing. One thing, though - you included ADVMAME in your list...I haven't encountered the problem with that emulator, but have with the Libretro emulators (LR-MAME2003, etc).
In the mean time, one thing you can try (again, this would only be for the Libretro emulators) is to enable the "Game Focus" after entering a game, which usually defaults to the Scroll Lock key (yes, a keyboard would be needed, though I believe you can remap the key within the Retroarch on-screen menus).
EDIT: Though enabling Game Focus can be used as a workaround, after further testing / playing I discovered that using the "Grab Mouse Toggle" instead is often all that is needed (Game Focus locks down keyboard inputs, which may be too restrictive depending on the hardware). The Grab Mouse Toggle defaults to F11 (+ hotkey), but can be redefined in the retroarch.cfg file (input_grab_mouse_toggle = "j", is what I'm using). Grab Mouse does what it advertises, and makes the OS mouse pointer 'disappear' and not interfere with the game's mouse pointer.
I could not remember which of the two screens contained the mouse axis. I think my suggestion for remaps would only apply to items in the Quick Menu -> Controls. Since the mouse axis isn't in there it must be the override that is supposed to save it.
I think there have been reports of some settings not saving correctly as expected. I read someone was able to save settings by opening the retroarch menu from within Emulation Station and therefore no ROM was loaded. Might be worth a try if you haven't already.
EDIT: I can confirm that neither overrides nor remaps will save a mouse index setting for me either.