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Yes, to make it a little clearer with less text ;)
I would suggest you use the RetroPie Setup script which you can start as explained and then:
– Update the script itself using the appropriate menu item
– Reboot (not needed, just to be safe)
– Execute a binary installation to get the latest binaries and the updated runcommand to select emulators
– Reboot
This may already solve your problem. If not:
– Update the PocketSNES emulator by using the command to update individual emulators and choosing “From Source”
If this doesn’t solve your problem please report back and I will help you compile a version yourself.
REMEMBER TO BACKUP :) (since these operations will potentially overwrite changes you made)