Are you trying to run a one tool wonder machine?
If so you likely don't need to use the TLO's 
If you're running a M6 with multiple tools then shoot me your script and I'll take a look.
You need to make sure the TLO (G43) is called before the zeroing of your Z axis to the material.
This way if multiple tools are called we are then just compensating for the difference between the tools rather than the entire tool length after zeroing.
You can see this happen if you have no TLO called and then zero your Z to the material, when your first G43 is called you'll be in a world of trouble.
I don't typically have the TLO called inside the M6 as it's normally called by the post in GCODE.
There are a lot of different ways to tackle this issue it's really what works best for you.
I really like to put a button on screen called "Job Setup" or something similar then call the TLO's and everything else I like prior to cutting with the click of a button.
So to recap, many years ago i was a cnc machinist, life change of career etc i didn't touch a machine for 17 years or so.
I got a Chinese 6040 about 4 years ago and had some success as a one tool wonder machine on mach3 then after a rebuild mach4. Just manual tool changes if anything.
I have now built a bigger stronger machine from scratch, and got an ATC spindle and a fixed tool setter. I haven't set up the carousel yet, i don't think i dare before i get the tool setter measuring correctly.
At the moment i use the code below, but the z0 is not setting up properly.
It may be my method, something i'm missing etc... not sure. In my mind the tool setter should update the tool length of each tool in machine coordinates, and it will have its comparison. Then set wpc z0 with any tool and the rest should compensate accordingly even tool 1. Am i doing it all messed up? i even manually set tool 0 and touched off the spindle face but still not working right.
Here is the code..
function m6()
local inst = mc.mcGetInstance()
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--change lines here to either auto rapid, or manually jog to a tool change position
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--Manual Lines. Uncomment line below to allow you to manually jog to a tool change position.
--local MyChoice = wx.wxMessageBox("Click OK, \nThen Jog to A Safe Tool Change Position,\nInsert New tool,\nThen Click Cycle Start.","Click OK to continue" , 16)
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--Auto Lines. Uncomment both lines below (and comment out local MyChoice line above) to automatically move to tool change position.
--Edit to include the machine coordinate values of that tool change position.
--AUTO LINES
mc.mcCntlGcodeExecuteWait(inst, "G53 G0 Z-5\nG53 G0 X200.0 Y20.0")--Move the Z to Home.Then to the X, Y Coords for our touch pad.
mc.mcCntlSetLastError(inst, 'Now in Tool Change Position. Hit Cycle Start!')
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local posmode = mc.mcCntlGetPoundVar(inst, mc.SV_MOD_GROUP_3) --get the current mode so we can return to it when macro ends
local selectedtool = mc.mcToolGetSelected(inst)
local currenttool = mc.mcToolGetCurrent(inst)
if selectedtool == currenttool then
mc.mcCntlSetLastError(inst, "Current tool == Selected tool so there is nothing to do")
else
mc.mcCntlToolChangeManual(inst, true);
mc.mcCntlSetLastError(inst, "Current tool == " .. tostring(selectedtool) .. " Previous Tool == " .. tostring(currenttool))
mc.mcToolSetCurrent(inst, selectedtool)
--local MyChoice = wx.wxMessageBox("Click Ok to Begin Probing the New Tool","Click OK to continue" , 16)
mc.mcCntlGcodeExecuteWait(inst, "G53 G0 X24.0 Y436.0")--
mc.mcCntlSetLastError(inst, "Probing in Progress!")
mc.mcCntlGcodeExecuteWait(inst, " G91 G31 Z-95. F150.")--probe the new tool
local probedz = mc.mcCntlGetPoundVar(inst, mc.SV_PROBE_POS_Z) -- Z Probe position in Machine coords
mc.mcCntlGcodeExecute(inst, string.format('G ' .. posmode))--return to pre macro mode G90, or G91
mc.mcCntlGcodeExecuteWait(inst, "G00 G53 Z0 ")--Retract
local NewOffset = probedz
mc.mcToolSetData(inst, mc.MTOOL_MILL_HEIGHT, selectedtool, NewOffset)
mc.mcCntlSetLastError(inst, string.format("Auto tool setting complete, Offset = %.4f", NewOffset))
wx.wxMessageBox("Toolchange Complete.\nTLO Set")
end
end
if (mc.mcInEditor() == 1) then
m6()
end
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