Does sound very much like the issue I had, I couldn't use the tab button on the keyboard to bring up the name menu.
After a clean format of the disk, making sure I used format with erase all data option, I reinstalled Retropie. Now everything works as it should. Keyboard name control button works in all games. I'm wondering if it was because when I first installed retropie I had issues with the screen, maybe i didn't erase all the data during format, and then had overlapping files.
Definately it works well now.
Worth a try, and only took me 10 mins, compared with the 3-4 hours playing about with various settings