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Based on Safe Mode comment, make sure the Karabiner kext (kernel extension) is uninstalled. Look in /System/Library/Extensions.

Check both your home directory Library/Application Support folder and the System/Library/Application Support folders and make sure the Karabiner folder is deleted--which should contain the private.xml document.

Safe Mode does not load non-Apple kexts so that suggests to me that the Karabiner kext did not get uninstalled. Not sure but I think the mods you make end up in that private.xml file. Lots of other files in that folder too. The uninstall scripts look like they should work but it's important to verify this yourself manually. Trust but verify....