Z tool offset help. Absolute coordinates change?

I have been reading here for quite some time and have picked up a wealth of information. Thanks to all who have posted for making their knowledge available to the community. PWallace of Mesa Electronics....I can't thank you enough for your time and patience, you are a man with wisdom beyond your years, You have helped me more than you will ever know.
Hopefully somebody knows what I may be doing wrong, or whether EMC has a glitch. I have seen quite a few articles on using tool length offsets with a mill and none seem to touch on whether the Z tool length offset alters the Z absolute coordinate. I have my limit switches set up just shy of my positive machine mechanical limits. Machine homing finds the positive limit switches, then moves -.200 away from the limit switches and calls this 0. this gives me a safe zone away from the ends of travel. A g28 will move all axis to this position -.2 away from the limit switches. A g28 Z0 will do the same for Z only and is what seems to be the norm for a manual tool change. What I am experiencing, and hope that someone can offer advice on, is when using tool length offsets the Z axis absolute 0 seems to change to a position above my limit switches. When I have a tool offset in use, and use a g28 or a g28 Z0 the Z will will try to move beyond the original absolute 0 position and trips an axis on limit switch error. (hooray for limit switches they work!!) I can't picture this as being normal behavior for EMC2 as it would render it useless for multi tool programs or a tool changer as the absolute Z height wouldn't be predictable, It would change depending on which tool offset was active. I assume that this is something that I am missing, but currently I can't see anything that I have missed so far.
Thanks again,
Steve

I have no idea if it is supposed to be that way or not, but if you use g53 z0 this should work. G53 will use the homed machine cooridnate system no matter what - although I have not tried it with tool offsets active. G53 is non-model, so no need to worry about changing back after.

G28 uses stored parameters as the position to return to:

"G28 axes will make a rapid traverse move to the position specified by axes, then will make a rapid traverse move to the predefined position in parameters 5161-5166.

G28.1 stores the current absolute position into parameters 5161-5166."

So it's going to wherever those points are and my guess is they are not your machine's physical zero points. As mentioned above... G53 G0 Z0 will take you back to exactly the original home position and will have no effect on the rest of your movement commands. I program that as the tool change position for my mill when I use TTS tooling and that involves tool-table offsets, it works perfectly be it a shorty end mill or a 3/8" jobber drill.

It sounds as if I need to get used to using G53 to return to an absolute 0 position on an axis when I have a tool offset active.
The 5161-5166 parematers, I am not famailiar with what you are referring to. Would you be as kind as to explain? Is this located in my
machine or hal ini, the area where I set my homing switch location, speed, final location and software limits? I didn't see anything which referred to the
parameters as 5161-5166 and assume that these would probably be a result of the settings I use when I set my homing up. Am I correct?
Thank you very much for the reply,
Steve

Well I absolutly cannot duplicate this now that I am trying to sort it out. The machine responds perfectly no matter which tool/tool offset is loaded. G91 G28 Z0 responds perfectly and sends Z to it's reference (tool change position) as well as using G53. This moving on to the limit switch was happening consistantly enough that I was sure that either I was missing something or that EMC 2.6 had a glitch. I have even tried resetting some tool offsets and was unable to duplicate the problem. Whomever it was that did the remote laying of the hands I sincerely appreciate it, thank you very much. on a serious note, to all of you who posted to help I thank you for giving of the priceless gift of knowledge. I learned a few new things about EMC from you. The only thing left to do is to go back and finish what I was doing and see if this resurfaces. Thanks again, and I hope that someday I can return the favor.
Steve

try to duplicate it by leaving out the G91.