I had the almost exact same problem:
I was adding widget items (of the same type) into a WrapBox, and for some reason sometimes the controller would just die after clicking around too much. The only thing that could refresh the input state was clicking manually with the mouse.
I tried adding delay, toggling visibility until click had been handled (Visible->click->NoHitTesting->clickdone->Visible), and other “wacky” stuff. Manual focus also did not solve it for me.
This is (so far) the solution:
But as Edgar Dijkstra famously said:
“Program testing can be used to show the presence of bugs, but never to show their absence!”
So until the bug shows up again, I just delay handling the click event until next frame 