@drylightn I just tested it myself and what I suggested is still correct. And you should be able to skip with any button on the controller, but that's isn't too important - that you can skip is.
Once you have configured every other controller but before you confirm the controls at the very bottom, use the D pad to move back up to the triggers. Then try to assign the trigger buttons, ensuring that they are set to +AXIS (Mine shows up as 2 and 5 for left and right triggers respectively).
Good in theory, but AFAIK the retroarch devs have no intention of implementing said feature in the short to medium timeframe. lr-fbalpha having it would be a lifesaver, there are a lot of 2, 3 and 4 buttons per player arcade cabinets out there that badly need it. What's the last lr-fbalpha version that fully supports it?
Is there a clrmame or other program that can check the samples files to let me know they are incorrect / incompatible?
The list of needed wav files is included in the dats i provide at https://github.com/libretro/fbalpha/tree/master/dats . Clrmamepro should be able to tell you if you have all needed wav files if you setup "Sample-Paths" in Settings, then check "Samples" in the scanner, it'll only check filenames though, not crc.
I was able to resolve this issue by putting the sample directory back into the original directory as stated.
After this, I updated lr-fbalpha again, how this time I did from source rather than binary. After this, I restarted EmulationStation and the samples worked perfectly again as they did prior to lr-fbalpha v0.2.97.42.
as far as i can tell, this behavior can be different depending on the BIOS. load up a neogeo rom for instance, and you will see a retroarch quickmenu >> options entry you can change to a few different button combinations (Holding Start being the default). then take 1942 for example in where holding start does nothing, and you must activate the service mode from retroarch quickmenu > options then restart the core.
also, there is a line in /opt/retropie/configs/all/retroarch-core-options.cfg
fba-diagnostic-input = "Hold Start"
that might be what you're after.
i'm not 100% certain on all this but i hope it helps point you in the right direction.