I use select+start to do menu just fine in E. Hakchi2 version has absolutely nothing to do with select+start for RetroArch options. If you run default NESC emulator or Canoe, select+start will not work, since RetroArch is not being used. If you reconfigure controls in RetroArch, you may also inadvertently screw up select+start shortcut. To fix this, simply uninstall/reinstall RetroArch. Again, hakchi2 has no impact on RetroArch shortcut
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You using my Core Set?
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Have you followed my latest EASY Sega-CD/ Turbografx-CD video?