G54 issue with limit switch

Hi I've recently added limit switches to my 3040. Before I was using touchplate to measure tool and set g54 z. After adding limit switches, I'm not sure what happened but when I load any program, it's is offseted much lower than it should be. Please look at screen below

Thx. Corrected

Ok lads, I've found it. The issue was caused by using
REMAP=M6 modalgroup=6 ngc=touch_plate

I've added it because after each tool change I would like to use touchplate to measure tool.
What I'm doing wrong? Any help?

Looking at your hal file, I don't see any links for limit switches for the Z axis:

Then in your ini I see you have HOME = 25 and HOME_OFFSET=25 yet you have not set any homing velocities, which makes me wonder how you home your z-axis?
 

You are right, I've commented out my limitswitch on Z as I thought this config could be the reason for my issue with g54. I will bring it back.
It's still not answer for my problem

Limit switches have no influence on your Z-offset but not properly homing your Z-axis certainly does.

That's interesting, could you please extend this topic?

sure:
linuxcnc.org/docs/html/config/ini-homing.html

Ok. I've enabled limit sw on Z axis and everything is correct.

After I add remap line, it is still wrong like on 1st screenshot. I've found out it is like that because of what I have in routines/touchplate.ngc.
Can someone point me where?
Is it missing G49? If yes where? 
Ps. When I press on button to manually measure the tool it works like a charm. But in connection with remaping M6 it cause an issue. 
All I want is if in gcode there is a tool change, lift z axis up, display message box to start manual change, measure tool in some position xy, measure using touchplate, display another messagebox with info to take touchplate, carry on the gcode. 

​​