What version of Mach3 are you running?
The recommended version with the ESS is ...062 and not 066
I suspect that your problem (in part) is associated with the input schematic for that board.... If you look at the at the attached screenshot extract...
You basically have a voltage divider being formed .... so when you apply 5V to pin 15 via a 4.7k resistor.... the voltage seen at pin 15 is 2.5V
<<<Ohms law >>>
by reducing the resistor to 2.2K.... you've increased the voltage to ~ 2/3rds of 5v, which is 3.4V
The datasheet for the Schmitt Trigger is here .... have a look at the switching voltages on page 5/21:
http://www.nxp.com/documents/data_sheet/74HC_HCT14.pdfI would suggest using a 1kohm resistor.... presuming you bought a pack of 2.2k ohm resistors.... I'd join tow together in parrallel (side by side) ..... NOT SERIES!!....
As that would make the high side voltage 4.05V which is well above the threshold voltages...
(really they should have used a jumper so you could have removed the 4.7K resistor).
You can set your debounce quite short as the inputs have capacitors (especially for your "probe" input on the ESS config screen) .... hence when the probling function starts the capacitor will be charged to ~ 4.05 volts (as per my calc above).... and when the probe is grounded the capacitor will discharge in about 470 micro seconds