The status message, "Axis 3 commanded while disabled" is because in the "Go To Work Zero" button, A axis is commanded to go to 0.00 as well as X, Y, and Z.
There are a couple of ways you can fix this.
1. Go into the screen editor and edit the goto work zero function in the screen load script to not include the A axis move.
2. Simply enable motor 3 in mach config. If you don't have using motor 3 this won't have any adverse effects, it will just be enabled.
I am using the ESS on a mill with Mach4 and I do get a little bit of funny noise while jogging, it messes with my spindle slightly and extremely briefly. I haven't messed with the ESS Config in a while, but is there a way to reduce noise on it? Maybe it is getting a false keyboard press?