I'll try this and see if there is any positive effect.
I saw it on Pac-Man (atarisoft version) while other games seem fine. I've been going through the list of games that work and don't work. So I've seen it a few times, but I don't remember which other games.
I also want to see if it effects the GUI as well because right now, it's un-useable due to how it seems to drag on the Pi so much. As soon as I get in to the GUI, I can check my controller assignments and see why I'm missing "UP". All other buttons and directions work fine.
I was thinking of switching to a Pi4, but I'm so embedded in the build of my Pi3 that until I finish it, it doesn't make sense.
Tried it with both frame-rate skips. Still unplayable, but better if using Autoframeskip. I checked all my settings for controls in Global and Local machine. Everything is set correctly, but I have no UP control in the game. Works fine in the GUI. Have no idea what could cause that.