I think @quicksilver might be right. On the PC, the actual start-up is done via $HOME/.config/autostart/retropie.desktop. Modify it and add a delay before emulationstation starts
[Desktop Entry]
Type=Application
Exec=gnome-terminal --full-screen --hide-menubar -e "sleep 5 && emulationstation"
Hidden=false
NoDisplay=false
X-GNOME-Autostart-enabled=true
Name[de_DE]=RetroPie
Name=rpie
Comment[de_DE]=RetroPie
Comment=retropie
Icon=/usr/local/share/icons/retropie.svg
Categories=Game