The arduino doesn’t have a strong enough resistor for what you’re trying to accomplish. Use a 100nf and some 680 and 10k resistors and you will be up and running in no time. I’ve proven it with many machines, up to about 40 sold (all worked) and however many have made their own. try it out you have nothing to lose here is the circuit for each axis. didn’t read anything about the noise suppression circuit built in now, but that’s good new if true, but still to pricey for my taste, maybe if it was available as an option instead of the regular boards before ordering, but hey early adoption comes at a cost. here is the circuit. Cause seems like one of your caps gave out and your getting a false signal from noise again.
Brian