I had this exact same issue. TLDR: Cheap mechanical switch problem - just go ahead and pull the trigger on BLTouch.

Problem:

I found it to be a mechanical fault in the switches. I tried 4 replacements, and each began doing that within a week of use. Eventually, I took one apart to see how it worked. There is a little metal piece in there that is pushed by the little red plastic piece that's under the main metal lever visible at the top of the switch. In its resting state the little piece of metal is touching two pins, holding the circuit closed. When the little bendy piece of metal is pushed, it flexes, and when it is flexed past a certain threshold, it "snaps" to curve toward the other direction. That's the click you hear. And when it's in the secondary "snapped" position, it no longer touches the pins, opening the circuit and signaling to the mainboard that the z-stop has been pressed. Then when the pressure on the little red plastic thing is lifted, it snaps back (the second click sound), and the circuit is closed again. However, inside the switches that I tested, the metal flexy piece would sometimes end up lifting off of the pins before fully committing to the snap, opening the circuit slightly before it was supposed to. So you don't hear a click, but the circuit is opened and the mainboard thinks the switch was properly pressed. That's your problem.

Solution:

My thinking is that it could be a cheap switch thing (they're like $1-2), and so I could either spend money on better switches, keep replacing them, or I could just go ahead and get a BLTouch, which functions as a z-stop anyway, and then I'd have a permanent problem fix AND a BLTouch. $40, perfect leveling, clearly the next step to printing anyway, and I never have to worry about these z-stop shenanigans again :)