I think i have similar problem. i can't change type of the machine and TV standard.
I always endup with Atari 800, 48k, NTSC.
If screen mode of my Pi Zero is 50Hz i have difficulity with the keyboard, like it running on max speed. Only game i have and can run with this setup is Jet Set Willy. Music is obviously at 60Hz sync and scroller have drops due to 50Hz screen and 60Hz emulation interference.
Changes made in emulators menu (F1) are saved properly. But the emulator never respect them. Or some of them. Because paths to ROM files and BIOS files are used so as the color settings.
Am i missing somehting obvious? It's seems to be caused by something in emul. execution parameters witch overrides the cfg values. I don't know. And i want my Draconus, believe me.
What i have already done:
Downloaded and installed the retropie twice.
Updated system and retropie
Changed, rewrited, downloaded from other people and saved from emulator. Config file Atari800.cfg.
Changed the rasberry screen mode to 50Hz and back.
Changed ROM specific (a button during game launch) config to 50Hz, added MACHINE_TYPE=Atari XL/XE, DEFAULT_TV_MODE=PAL
and... nothing.
thanx guys.