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That is a very strange situation I haven't heard of before. This sounds like a bug. Please attach a screenshot of the joystick axis screen where you see this issue and a copy of your log.txt from the main X-Plane folder.
For now, you might be able to work around it by setting those button axes to "none" so that X-Plane doesn't use them. Try setting up the button assignments like usual and see if that helps.
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