@mitu . Thanks I'll give it a shot.

Thanks everyone!

I found the solution for my setup. In short, the solution was to use the audio on my TV rather than my home theater system.

My Setup My setup is a small home theater, not a dedicated display for retro awesomeness... Raspberry Pi 3 HDMI output to TV TV volume all the way down Optical S/PDIF out to Bose speaker system

As it turns out, this is okay for some MAME games, not frogger or most anything that needs samples. It sounds like some of the audio durations are too short to come through the system. Perhaps it needs to un-mute the Bose amplifier and fade in, but by then it's too late to hear anything more than a slight pop.

Solution Raspberry Pi 3 HDMI output to TV Use TV volume (don't route audio through home theater, it can be plugged in but not used)

I put all of the config files back to default, I think..., and all of my mame and nes games seem to sound good with some quick testing.

All is well in retro land. I hope this helps someone else!