I am having somewhat the same problem.
Jogging from keyboard works fine, but
Mach 3 ignores some gcode commmands ,but not others. It will ignore
G1 x-1
and run the next line-
G1 y3
seemingly picking the lines to run at random
it also draws lines on the computer screen incorrectly, leaving out the ones which are ignored when running the machine.
The machine was working properly last week.
What have I done, or do I have to reload a new copy of the program