If adding a nut works for you, that’s fantastic! However, I wasn’t able to replicate your success here.
My theory about what’s happening is that when the knob is seated at its maximum depth, the 4 internal support structures that grip the encoder shaft which extend to the bottom are now close enough to the threaded metal barrel such that when the knob is pushed to click, the travel is now constrained just enough to prevent the switch from making an electrical connection, even though the part of the switch that gives that physical “click” feedback has engaged.
Adding some kind of spacer to the end of the shaft, like I’ve done here with a few layers of electrical tape cut to size, prevents the knob from seating quite as far down, which seems to give just enough extra room between those support structures and the threaded metal barrel to allow the click to work reliably. However, this is not a long term solution, because the tape may compress or otherwise deteriorate. A better solution would be a hard plastic or metal spacer, or different knobs.
Either way, I’m concerned that adding a nut over the top of the faceplate doesn’t address the real issue, and is somehow solving the problem indirectly, by creating extra stress on the encoders or PCBs to which they’re mounted, which could lead to longer term issues.
But that’s just my $0.02!