Maybe check that you don’t have more than one physical control mapped to each of the commands.
Having a physical switch on one of your controllers mapped to your gear/spoilers/flaps, by position rather than as a toggle, and you don’t know about it, might prevent it from moving away from that position when you manipulate the physical control you do know about.
As to why it’s just started, that might be because the state of the “unknown” switch has been changed or it might be that a recent update has introduced the “unknown” mapping.
It shouldn’t take too long to check whether this is the cause or not. Good luck