Confirmed that the Paddle/Red are connected to “S” and clamp/black connected to “G”
I’m happy trying to reflash. I’ll take a screenshot just in case, but are all of my customs settings stored in config.yaml and preferences.json?
I’m attaching my config.yaml just in case 
config.yaml.zip (2.1 KB)
This is important, the static from your hose can mess with inputs.
What customs settings specifically?
Take note of your offsets for Y and Z and that should take care of alignment and squaring, and your changed steps per mm. although the config can easily be restored.
looking at your config you changed the Y steps per mm, but not the X. Obviously this has nothing to do with your issues but typically if the Y is different the X would be as well.
My vac hose is not currently grounded. I will do that; it needs to be done. While that will prevent other issues, it seems like this can’t be the root cause of this issue since one gcode consistently works and one doesn’t with an ungrounded hose; i would expect inconsistent results or consistently failing to probe properly. Is my logic sound, or am I missing an important detail?
i guess it was just the offsets. i was more asking if all the changes one can make from the WebUI get saved to config.yaml and/or preferences.json
Yes, except for some settings like for Wifi are stored separately (not in a file). You can use $S to output those details to the terminal. You can skip the $Grbl settings and unless you’re completely wiping during a reflash, they persist. That won’t give you any passwords though.
This might be a long shot, but the yaml files are extremely sensitive to spaces. I noticed that your file has spaces after things like stepping: and uart1: etc. Chances are you updated the settings in the WebUI and the save changed all that. Although, it wouldn’t be the first time that broke a config.
Try this version. The only meaningful difference in your config from the default is the Y steps per mm update. This is the default JP3 config with your steps per mm update.
config.yaml.zip (1.5 KB)
Shoot you are good. I only saw them in the macro section. Next time I will try a space search, the highlight in vscode is kinda hard to see.
A reflash seems to have done the trick!
@jeyeager I didn’t see your reply before testing and reuploaded my saved config.yaml, but everything seems to have worked 
but i’ll make sure there’s no cruft in there just to be safe.
not sure what to mark as the solution for this topic, but i’ll definitely remove the solution that I previously marked. I also noticed that the WebUI is now at 3.0.0.5 whereas I was previously on 3.0.0.6. No idea if this fixed the issue, just wanted to point it out.
thanks all for sticking with me til I got this figured out! now I can go cut me some struts!
Interesting. Stick with what you have for now. If it works no reason to change.
Glad that resolved it! The WebUI wouldn’t have made a difference. And it seems the config.yaml didnt matter either. It is odd that it had a bad flash but it’s not unheard of.