Question Re: Work Offsets

I had some odd behavior on an EMC system running BDI 2.16:

I spent the last two days PID tuning to get the axes running
cleanly. They're running cleanly now, and in the process I had the
opportunity to set up and run a number of toolpaths, mostly
prototyping in pine so a tool crash wouldn't be disastrous.

Today I tried to run an actual part. I used an edge finder to
indicate in the workpiece, and set my zeros by right-clicking on
each axis in turn and setting it to zero.

When I ran my program, it proceeded to crash the tool into the
workpiece (even though the first move is to go to (0,0,0) and raise
the quill to 2.0" off the top of the workpiece.)

I carefully checked my zeros and loaded a new part. Same behavior,
only this time it snapped the end mill off.

Before changing a tool and crashing it again, I played around with
it.

In MDI mode, if I typed "G0X0Y0Z0", it would go to (0,0,0) in the
relative coordinate frame. If I ran the program, it would attempt
to go to (0,0,0) in the absolute machine coordinate frame (the Z
value of which was well inside the workpiece).

I stripped the entire header off the program file so it starts with
that "G0 X0.000 Y0.000 Z0.000" statement. Same behavior.

What am I missing here? I thought MDI and running a program was
essentially the same thing. I didn't know one would run in one
coordinate frame and one would run in the other. I'm REALLY puzzled
why this behavior didn't show up during the two days of PID tuning I
did.

I could seriously use the help. I'm dead in the water, and not
really interested in busting any more tools or driving any cutters
into my vise or mill.

Tom