Only common thread I have for this is it only seems to happen, at least for me, with AH. Irregular momentary derps which often times, but not every time, result in my stick mappings up and disappearing. In IL2 and MSFS I don't have this issue. Can't say about DCS as I don't play it. If it's happening on the desktop, I'm not noticing it. Because of this I'd focus on AH. Something in the game is calling for something that probably isn't there anymore from 267 updates ago in the rest of the internet. That's my take on it anyway.
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