5Axis Kinetic from 2.8 on 2.7x

Actually I still have doubts that you are indeed running switch-kins-branch as there is no reference to it in the terminal output.
Have you tried to switch kinematics in the simulation?
If you can use M428 and M429 to switch betwee identity and 5axis-trt-kins in the simulation then you know you have it setup correctly.

[edit]
I'll post the terminal output of my machine when I start the 5axis-trt-simulation tomorrow.

What does this give you? (run after you set the environment with source.. etc)

$ git branch | grep \*

So, it seems that you have not actually built the switchkins-branch because I just built the switchkins-branch and when I do:

user@linuxcnc:~/linuxcnc-dev/configs/sim/axis/vismach/5axis/table-rotary-tilting$ linuxcnc xyzac-trt.ini

I get this:

I suggest you do this and try again:

If you home your machine and then set the zero positions in say G54 the offsets should be saved when you shut down LinuxCNC. You do need to home your machine each time you start LinuxCNC though.