Call external subroutine not working in recent versions of LCNC

Ok.. I do have an issue here.
I am running Axis 2.8.0 pre1-4546
I have a subroutine to zero the z axis, and placed it into the ncfiles section
When I boot up, and home, I try to run the HAL button that I have tied to it, but it doesn't work
I can use the MDI window and execute the subroutine ( o<toolchange3> call )
AFTER I execute the subroutine via MDI window, I can now use the HAL Button to zero the z axis... ok, weird ...
I now load a program from the share
I can no longer zero the axis via the MDI button OR the HAL Button ..

All this worked fine before I updated to the new LinuxCNC last year. I had to update because I have tied X axis motors, and the update worked well for that. So, If I load the zero routine manually from the files.. it works...

Can anybody give me ANY lead on what to do? It doesn't appear to follow a rights issue, but maybe????? And what documentation if any could I supply here????

shipmodeller@LinuxCNC:~/linuxcnc/configs/my-mill$ uname -r
3.4-9-rtai-686-pae
shipmodeller@LinuxCNC:~/linuxcnc/configs/my-mill$ lsb_release -a
No LSB modules are available.
Distributor ID: Debian
Description: Debian GNU/Linux 7.11 (wheezy)
Release: 7.11
Codename: wheezy

It was acting "off" last year when I loaded up the new Axis, but then I had a few months off while playing with my new 100W Laser, then travel, holidays then surgery. When I got back on it this month, it had one or two more updates, than I started to really use it again. That's when I noted this problem for sure, and had time to reproduce it. It is quite reproducible. I am willing to try whatever, it is almost unusable if I have to restart it every time I do a tool change. It almost looks like a file rights issue.. but then again.. I am not familiar with the source.

I did a quick look at your link.. I didn't do any editing.. The steps in my note are the only things I need to do to reproduce it from startup. I don't want to go backwards on LinuxCNC because of the dual drives on the X axis.. it works great on the new versions, but this process of having to reload on each tool change is bad. And yes, I could manually set the bit each change.. and I have.. but come on.. this is a defect of some kind. Thank you.
How can I proceed to help solve this?

Pretty sure I supplied those files before .. and remember.. what you "simulated" did not seem to address the issue.. but I thank you for your effort. I have put up my ini file, and the hal files for you to look at. I don't know what is going on, I suspect rights issues... I can load those files via midi all day long, UNTIL I load up another file, then I lose it. So, the main question I will pose again, should I push this as a defect, and if so, what documentation should I upload? Very big thanks...

Right now, I am getting around all this by loading the toolchange program manually for each tool I need. PIB..

Well, the metal touchoff .. was working in the prior release.. yes. ( 0 added for offset.. ) So when I did wood, the .625 was added. When I did metal, nothing was added to touch zero.

So.. the number 1 issue as reflected in my original post is:

1: From boot, I can go tot he Midi panel and execute the o<xxx> call tool change without problem.
2: The button doesn't seem to work till i do that .
3: But, once I load a GCODE file into the system, the midi command won't find the toolchange file anymore and the button no longer functions.