Ok I just did one more test and I downloaded the Atari800 core from the retropie setup and it does have perfect sound quality (audio coming from my left speaker only, though), and it uses the same BIOs files than the lr-atari800 core. Is this normal? I want to use the lr-atari800 because of the keyboard being mapped to the joypad, or maybe if it is a way to get into the Retroarch menu in Atari800, and the set up my gamepad being Atari Joystick?

Thanks in advance!

please ignore/delete this thread (sorry) it seems I've worked it all out using SGM-V2.01.sf2 and i'm cool with that. Apologies for wasting anyones time.

A few suggestions

Make sure you have a good power supply. Low power will cause the RPi to throttle down causing all sorts of glitches

If you're using the 3.5mm jack, better get a USB sound card. The 3.5mm is known for it's noisy output.