Seems there may be one more config to change according to this post:
http://blog.petrockblock.com/forums/topic/how-to-get-games-to-be-169/#post-100190
I usually use a program called winscp to edit things, or if you have a keyboard you can plug in you can go into the terminal and edit it with the command sudo nano /opt/retropie/configs/all/retroarch.cfg then locate the lines you need to change and press Ctrl+x to save. Floob has a few videos that outline using the terminal and editing configs.
This video shows how to save configs. It is about controllers but it should apply to other config changes too.