I think I (and others) have the same problem with the Vice emulator.
Can you try this:
1. First exit Emulation Station through the options menu.
2. In the shell screen that follows, type ‘exit’+enter. Now Emulation Station will reload.
3. Now just start your emulator from ES and see if ES is reloaded properly when you exit the emulator.
This method works on Vice. If it also works for you, then maybe this can the Retropie developers help to fix the issue.