How is LinuxCNC connected to the VFD?

Direct hardware control, with an analog speed command and start/stop signals 
from a parallel port?

Or serial communications using a HAL driver specific to that brand of VFD?

Or Modbus using the generic LinuxCNC HAL Modbus driver?

Or Ethernet using ??? driver?

That is critical information - I don't recall seeing it anywhere in this 
email chain, but maybe I missed something in the first message or two.

The core of LinuxCNC (GUI and motion controller) doesn't communicate with
the VFD at all.  LinuxCNC reads and writes to HAL pins, and those pins are
connected to some driver that in turn talks to the drive.

So there are two things happening here:

1) The core of LinuxCNC manipulates the HAL pins differently when you
use M3 or the MPG compared to when you use the on-screen buttons.

2) The driver and/or the VFD itself responds badly to the HAL pin activity
from the on-screen buttons.

I think the first step is to figure out item 1.  Set up halscope to observe
all the spindle-related HAL pins.  Capture and save shots of it working
correctly when driven by M3 or the MPG.  Then capture it failing when
driven by the on-screen button.  Study the screen pictures and figure
out what is different.  Maybe the difference makes sense given the
context, maybe it is a bug in the core of LinuxCNC.  Post your findings.

If the difference makes sense, then the problem is in the driver or the
VFD.  If we know exactly what driver you are using and how it is 
connected to the drive, and we know exactly what the HAL pins going
into the driver are doing, maybe we can figure out what is wrong.

-- 
  John Kasunich
  jmkasun...@fastmail.fm

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