Double check that a button or key didn't accidentally get assigned to lower the gear and / or flaps. That sounds most likely if it is happening with every plane. You can also check fairly quickly by resetting to default preferences:
Move the preferences folder (found in the Output folder) to the desktop, then restart X‑Plane and default preferences will be restored. If the default preferences do not fix your problem, you can simply replace them with the folder you moved to the desktop and restore your personalized settings.
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