That seems odd from a top-dollar laser, so something is not right.
The obvious question: does homing work correctly?
The laser head should trundle off to one corner, bump the home switches, back off, bump them again. and stop at exactly the same position every time you turn the machine on or reset the controller.
Set the manual pulse parameters for about 10 ms and 30%, put a scrap of MDF under the home position, home the machine, set the focus, and fire a manual pulse. Home / focus / pulse it half a dozen times, turn it on and off, reset the controller: all those pulses should produce exactly one pinhole in the MDF at the home position with absolutely no outliers.
If it’s not what happens, then take advantage of Thunder’s US support staff, because your machine is not working correctly right out of the shipping crate.
If the laser produces a single pinhole, then the problem is likely to be your technique.
Switch to Absolute Coordinates
and never look back. That makes the LightBurn work area match the machine’s platform, so when you position a layout, you know exactly where it will appear.
The fixtures should be mechanically aligned to the platform so they get clamped / screwed / attached at exactly the same place every time, without having to think about it.
Put a crosshair target in each corner of your fixture so you can verify their placement:
With the fixture installed, use LightBurn’s Click to Move
tool to put the beam exactly in the middle of a target. Fire a manual pulse (*) and the pinhole should be invisible in the middle of the crosshair. Do that for two diagonal targets and you know the fixture is both positioned and aligned.
If that’s the case, then you’re ready to start engraving / cutting / whatever.
I use Print and Cut
with those targets so I need not worry about exact fixture location, but I’m not in production and you likely don’t want to put that much effort into location.
It’s always touching to see such innocence. 
Most likely it’s in fine shape, so make up some targets and verify the alignment so you’ll know what things should look like, before the time comes when you must tinker with the mirrors.
(*) If you have a trustworthy red dot pointer, you need not do the pulsing, but you should verify the pointer alignment with a pulse every now and again.