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

When did it stop working? I wonder if this fix has broken something?
github.com/LinuxCNC/linuxcnc/issues/455

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?

shipmodeller wrote: 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 wasn't suggesting that you had edited the file. I was speculating if the fix for the editing problem might have broken something else.

I have tried to create a simulated machine with a HAL button and an ngc routine triggered by an MDI_COMMAND and it all works.

Maybe you are using a different "HAL Button". Can you explain how your O-sub routine is linked to HAL?