I actually discovered a very easy fix for this as i was having the same issue. My sixaxis remotes accelerometer was causing me to enter the menu screen every time i launched a game.
go here
opt/retropie/supplementary/runcommand
first make a backup of runcommand.sh
sudo cp runcommand.sh runcommand.sh.bak
then open runcommand.sh
sudo nano runcommand.sh
find this line
IFS= read -s -t 1 -N 1 key </dev/tty
Then modify the “-N 1” to “-N 0” so it should look like the below.
IFS= read -s -t 1 -N 0 key </dev/tty
This will tell the script to look for 0 characters being pressed (and therefore you will never enter the menu. This will probably get overwritten when you update so you might need to modify it again.