Ok, SNESDev is also running. This might be a cause for the problems. You can disable SNESDev with the RetroPie-Setup Script or directly from within the downloaded SNESDev-Rpi repository that you can get from https://github.com/petrockblog/SNESDev-RPi. Within the SNESDev-Rpi folder you can call sudo make uninstallservice to uninstall the SNESDev service.