I don’t know if this is the same issue but I noticed similar behavior recently (after the update to 1.15.8.0, but it might have started before then). I discovered the problem was with pop out windows. If I opened the NAVLOG window, for example, and popped it out to its own window, and if my cursor hovered over the pop out window or make it active, my yoke and throttle quadrant stop working.
This does not happen when other third party windows are activated. Other than keyboard entries, the yoke and throttle quadrant continue to send input to the simulator then.
MSFS hasn’t always behaved this way, so it must be something introduced in a recent update.