I had the same issue with my Rpi3, the update with Zigurana’s suggestion worked for me.
It’s faster and easier to just use a USB drive to tranfer ROMS BTW. Here are the steps just in case you haven’t tried it.
(ensure that your USB is formatted to FAT32)
first create a folder called retropie on your USB stick
plug it into the pi and wait for it to finish blinking
pull the USB out and plug it into a computer
add the roms to their respective folders (in the retropie/roms folder)
plug it back into the raspberry pi
wait for it to finish blinking
refresh emulationstation by pressing F4, or choosing quit from the start menu