Thanks @PCW, those settings got me on the right path. I have decided to ditch the flip flop IC and just go back to the periodm solution with the full scale sensor reading as the signal does something more logical (maybe one day I'll sit down and try to figure out what is going on...)
I've done all of the frequency to voltage scaling inside a custom component, which I hope to add other functionality to like dynamic probing. I'm kicking around the idea of not probing down to the work surface, but instead to a set capacitance level (voltage). This should in theory be quicker and not have to worry about material bouncing after probing. I did several repeatability tests with the "probe-test" button in qtplasmac and found that the probe speed greatly affects accuracy (no kidding). But the sweet spot with cut quality is quite small, so I'm considering an alternative approach to probing. The dynamic part of this is that while say 50 volts (or whatever it is scaled to) is an appropriate cut height, I want to probe down to this height and start cutting right away. I would still want to catch nozzle tips, which would show as 0 volts, so the ohmic-probe input value would need to adjust dynamically based upon which state plasmac is in.
I realize that this may not be a great approach for thicker materials which require an additional pierce height, or materials with two stage piercing. I'm also new to this, so I'm learning as I go.