I didn’t see you mention anything about "RUN FROM HERE" in your post but it was brought up.
To possibly help out I can tell you two way I am able to recreate your issue:

- You cannot "Regen" a toolpath after issuing a "Run From Here" till after the machine moves in to position (know issue).

- Always put "If (Isloading() = false Then" in your macros or Mach will read them while loading a file or a "RUN from Here".
There is now an option in the "Gen config" to ignore Mcodes while loading..but it best to have this in you Macros or any VB to make sure

I will have to try this. 

I'm not using any macros, plug ins, or anything that would mess with any settings.  In fact it's pretty much a Plain Jane install, then run code.

So I am reviving this thread, as I had this exact problem. (1st official post, BTW!).

Initially I thought that it was the 84,000 lines of g-code that broke Mach 3, as it didn't want to generate the tool path when I loaded the g-code. Then I decided to actually connect the breakout board to my PC running Mac 3, and voila, it worked!

So in my case, the fix for this was to connect the breakout board to my Mach 3 PC.