I have just fixed the Fault
runcommand-onstart and runcommand-onend scripts
Runcommand can execute an user script before the game launching (runcommand-onstart.sh) and after exiting the emulator (runcommand-onend.sh). Both scripts must be placed at /opt/retropie/configs/all/.
These were the settings. I changed them to 1024 768
fbset -g 320 240 320 240 8
fbset -g 320 240 320 240 32
Not sure how these are changed, but hey :-)