I think that John’s mention of the plist might sort this out.
You might try deleting the ‘shortcuts.plist’, and then restart SU so that it can regenerate a new one. . . which should also restore the default KB settings. . . Albeit, in a heavy-handed manner when compared to the Reset All option.
The link below more or less outlines my own previous experience with this… and I hope it’s helpful in your case too.