Found one minor issue where I forgot to log input signals in debug=true on pairs() iteration ( https://github.com/mk-fg/games/commit/782589e , will bundle something else in there).
But can't seem to reproduce the issue with the input signals that you're having, unfortunately - they all seem to work as expected, and match stuff displayed on the right (which is built via same cn_wire_signals call), so don't know what else to check here.
I'd probably check if it's only this one combinator that is bugged, try different code there (like simple "if signal then log end" stuff), see if that works, and if not, check same on other combinators, then try replacing this one, to see if it's state is bugged somehow, or save/reload the game.
Though iirc only things that persist on these in globals (between reloads) are loaded code string, gui text (can be different from loaded code), entity ref, environment table, outputs, and whatever open gui state(s). There's nothing persistent related to input signals, so can't think of why they might be bugged on one particular combinator atm.