What's in the boot partition of the SDcard ? It seems only config.txt is being read and the other files are either missing or corrupted - including the firmware files needed to start the boot. Did you get any errors during the update ?
You can copy over the files from a good known boot partition, but they'll have to match the kernel you have installed. You can save your sdcard as an .img file, then re-install RetroPie and do an update again. Save the boot partition contents, restore your initial image and copy over the saved file from the correct boot partition.