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That is really odd- you have baffled as well. The only other thing I could think of is maybe just writing the retropie SD image directly to the SD card- that way you can at least rule out your hardware (harddrive or USB hub or adapter) I’ve never done anything with external harddrives or mounting them for a raspberry pi so I’m afraid I’m not much help when it comes to custom setups (you could also wait for the latest build in the next couple weeks because the controller module for emulationstation has changed so it might also affect how your controllers and keyboard respond.)