Tandem Z axis suddenly homing in opposite directions

Are you sure -0 is valid? I do not think -0 is a negative number
(once parsed and turned into a sequence number) so would not
force synchronized homing

Did you check that (via halmeter or halshow)

joint.3.home-sw-in
and
joint.4.home-sw-in

change appropriately when you activate the Z home switches?

I was too quick to call this resolved.

Once I had the machine running I loaded up the attached g-code for a zero clearance insert and couldn't get it to start. I thought perhaps because I removed the tool change in the pncconf earler but no matter what I did the machine wouldn't move under its own command. I tried restarting LinuxCNC which then meant I needed to rehome. Upon hitting the home all button the damn Z axis started going in the opposite directions again.

G-code attached along with the current ini and hal files

Here's precisely what I did.
1) loaded Linuxcnc
2) home all
3) moved Z down
4) moved X
5) touch off X (touch off button)
6 Moved Y
7) touched off Y
moved Z down
9) touched off Z
10) pressed run and nothing happened, no errors, no movement, no noise

Thoughts? This is really frustrating.

Minus 0 is what pncconf writes every time I save the config. I'm not familiar with Halmeter at this point. I'll have a look at how to use that.

Why do you think -0 is a valid home sequence number for synchronized joints?

Edit OK if pncconf uses -0 that's a pncconf bug
(integers like sequence numbers cannot represent -0)

I would renumber the home sequence number starting at -1 for Z

This may not fix all of you issues but will at least
force the Z joints to do synchronized home moves

I'll set it to -1 shortly. Grabbing some dinner.

Is it a problem that Z and one of the other joints is also -1 or can all joints be -1 in theory?

If you wanted Z to home first you would use -1 for Z and higher numbers
for the other axis , using negative numbers for joints that need to be synchronized.
That's why I said you would need to renumber the homing sequence numbers.

For example If Z must home first but X and Y can home at the same time:

Z joints home sequence = -1
Y joints home sequence = -2
X joint home sequence = 2