30 Second timeout before opening and E-Stop button not clicking...

No, sadly not!
I tried various other things too, but nope.
I am going back to do a completely new install from scratch of Linux, etc. which requires a SSD shuffle between computers.
...

if the sim opens and works (ie.. press estop, press power, press ref all and it works) its not an installation issue. the problem would be pointing to your machine (milling machine) configuration problem, maybe post your configuration to github and share the link here so we can have a look and maybe help get you sorted out. having the configuration on github is nice because you will always have quick access to it for reference or troubleshooting even when not at your machine pc.

Okay, my two setups are here:
github.com/TriodeGirl/LinuxCNC
The AXIS one works, the Probe_Basic is the issue.
I am using a MESA 7i96s board set at 10.10.10.10
I have E-Stop enabled, and am supplying a suitable active signal to the pin input. This works under AXIS.
Many thanks.

first thign i see is you ar emissing the postgui hal file that is required. you need to uncomment the ini for that line and copy over the probe basic post guiio hal file as is stated in the docs.

it looks like you may have missed a few steps, go beack through the machine config section in the docs really carefully and make sure you have done all of the steps accordingly and i think you will find things will work as expected.

kcjengr.github.io/probe_basic/machine_config.html

So installed a new Debian 12 Bookworm Linux on a new SSD exactly as per instructions here:

kcjengr.github.io/probe_basic/probe_basi...develop_install.html

... and I cannot install LinuxCNC because:

dpkg: dependency problems prevent configuration of linuxcnc-uspace:
 linuxcnc-uspace depends on libboost-python1.74.0 (>= 1.74.0+ds1); however:
  Package libboost-python1.74.0 is not installed.
 linuxcnc-uspace depends on libboost-python1.74.0-py311; however:
  Package libboost-python1.74.0-py311 is not installed.
 linuxcnc-uspace depends on libgpiod2 (>= 1.5.1); however:
  Package libgpiod2 is not installed.
 linuxcnc-uspace depends on libmodbus5 (>= 3.1.4); however:
  Package libmodbus5 is not installed.
... etc

I have been round this loop before, which is why I installed the combined Bookwork and LinuxCNC package; but then Probe basic doesn't work.

If the sim runs probe basic works. Your mqchine configuration was wrong.

As i stated in the fb group. You can i stall the deb with gdebi instead of using dpkg and it will find the missing dependencies. You seem to be making this much more difficult than it needs to be.

Once installed, run the probale basic sinulation from the Linuxcnc application chooser. That tells you definitively if the installation is correct. You should be able to run probasic take it out of e-stop select power Hit The ref all button and watch the Sim work if you can do this the installation is correct.

Now your actual EMCO configuration is wrong it needs to be fixed that will never run the way it is until you go through the machine configuration section of the docs in the pro basic documentation website and make sure that your machine configuration is set up correctly.