I have problems with the Z zero. I put the offsets for x and y and size the tool's high in order to get the zero for the work, so my offset table has numbers for X and Y and zero for Z, and my tool table has the H put in inches from the zero or home position, to the top of the stock in negative units . So, when I told the machine  "go to zero" it goes exactly in position with the tool almost touching the top of the stock. The problem is when I start the cutting: the machine goes below the high specified, and cut the stock thru. Is like the work's Zero goes below the top of the stock to the bottom of it. It shows it in the Z DRO. I don't see nothing anormal with the Gcodes. Those are:
G20
G0 G17 G40 G49 G80 G90
T1 M6
G0 G90 G54 X.37 Y.3074 S2200 M3
G43 H1 Z2 (The H1 and the G54 are checked ,H1 has a negative value in the tool table)
Z.1
G1 Z-.35 F4
I believe with the command G1 Z-.35 the tool has to go .35 inches below the top of the stock which is the zero for Z ,but it goes like the zero was the bootom ,not the top of the stock but if I don't put any Gcode and push "go to zero" it goes to zero normally. Please help ,I'm turning crazy.

Did you ever get an answer or solution to you problem.  I am having a similar problem.  All works well as far as G 52 work offsets, and the referenced tool going to the G52 zero position when I select "Go to Zero".  But as soon as I load g code from BobCad some how the tool offset gets dropped and if I don't stop the Z axis it will go all the way through the machining wax I am playing with. I have already ruined a diamond tipped engraving tool as a result of this.  I have checked and rechecked the g code and BobCad says the G code is fine and that it has to be a Mach 3 setting some where.  I cannot figure out where. 

Is ther any way that you can talk to a real live person at ArtSoft?  If so can someone give me the number so I can get this fixed and get on with what I bought the machine and software for.  Thanks

You need to learn how tool length offsets work.

If your code is applying an offset with G43, you need to make sure that the offset is already in effect when you zero the Z axis.
I think that most people that use G43, use a reference tool and zero that to the workpiece. All other tool lengths are based on the difference between them and the reference tool.

The tool offsets are all in the tool library and the g code shows the correct "H" tool being called so the G 43 should work but what happens is the tool offset in Mach 3 gets turned off somehow.  But before he code is loaded I can put new tool numbers into Mach 3 and enter them and they all find the G 52 work offset zero point which confirms that the tools were measured correctly and loaded correctly into the tool table. 

Greg

Make that G54 work offset

But before he code is loaded I can put new tool numbers into Mach 3 and enter them and they all find the G 52 work offset zero point which confirms that the tools were measured correctly and loaded correctly into the tool table. 

It doesn't confirm anything if you're not doing it right.

Tell us exactly how your confirming that they are correct, and don't leave out any steps.

Ok here goes. 
First turn on computer and open Mach 3.  Then turn on machine control but not spindle power.  I then "ref all axis" and confirm that the machine coordinates are all at zero.  I then insure that work offset 1 is selected which is I believe G54 work offset.  I then insert my work piece ( square of machinable wax) in the table vise.  I have a three axis touch probe that I use as tool 99 and have it hooked up to break out board pin 10.  The probe is in a tool holder and I measured it with a vertical digital indicator on a granite block.  I believe it's measurement for protrusion from spindle is 6.515.  I have inserted that value in the tool table for tool 99, along with the tip diameter of .090.  I then install the probe, tool 99, into the spindle and tighten it up.  I plug the probe into the connection to the BOB and go to the offsets page of Mach 3.  I sure that tool 99 is selected and that the tool offset length and diameter show correctly.  I then jog the probe Down to the -x side of the back edge keeping it abou .25 away from edge.  I the select the -x touch spot on the offset screen and that causes the table to slowly jog toward the probe until it touches the tip and that causes the x coordinate for work offset 1  to become zero.  I do the same thing with the probe for +y side of the material and also for z.  Those actions as described have zeroed the back left hand corner of the material.  I then jog the probe up and away from the material, insure that tool offset is still highlighted and then select "go to zero" on the program page.  The probe moves and zeros to exactly the upper left hand corner of the material whic is x0, y0,z0.  Then I remove the probe (tool 99) and select a 3/8 EM which has also been measured with the vertical scale on the same granite block.  The tool length extending from the spindle and diameter have been entered into the tool table under tool number 3 and saved.  I place tool number 3 into the spindle and tighten.  I enter tool number 3 into Mach 3, insure that tool offset is still highlighted and that work offset 1 is still the selected work offset.  I then select "go to zero" on the program page and tool number 3 goes exactly to the upper left hand corner of the material at the x0, y0, z0 position.
So that is how I get to the point before installing G code.
Does that sound correct?