Can you post a screenshot of your rotary settings window?
Are your engravings coming out to scale?
Have you tried loading an older preferences file?
Have you tried running an interval test from the laser tools window?
Did you disable rotary in the rotary setup window when you went back to flat?
I don’t have a 2Trees so just speculating.
I have not tried resetting lightburn yet not sure how to do it.
I ran some more test today with laserGRBL and with lightburn. I’m still getting lines with both programs on the rotary chuck. With out the chuck the lines are almost comletely gone unless you have a magnifying glass, But the edges of the materials test grid boxes have waves in them. Here are some more photos.
Here are the settings for the Rotary.
Yes my engravings are a scale
What do you mean by older preferences files?
I posted some materials test today
I respectfully disagree about not changing scan angle on a rotary. I am NOT a guru or a developer, but on my set up I get much better results engraving on a 90 degree angle than I get on a 0 degree angle.
I am on a 5w diode with a rotary chuck. At 0 degree angle I get a corduroy texture. At 90 degree I get a smooth surface.
It works for me. And it may address your problem.
Give it a try 
A chuck is a different story 
With a chuck you don’t have slipping of the objects, so the scan angle doesn’t matter. The advice not to change the scan angle is for rotaries, not chucks.
Interesting, thanks for the additional photos.
Your main issue seems to be only really be showing at the rotary (the skipped lines), which appear to be regular despite changing line interval or scan angle - is the interval of the problem the same as gear gogs/belt teeth at the rotary?
The other pic (IMG_1669) on the flat with the ‘boxes not square’ and where you labelled the ‘Box is wavy’, is possible a secondary or downstream issue since it also seems to appear at the rotary (IMG_1664), so you may want to check the laser module - mount/head assembly/optics, for any looseness that might contribute to a front-back wobble.
It might be useful if you ran this backlash test program (on the flat):
Backlash.lbrn2 (73.5 KB)
Post the results here please.
Check for the hallmarks of a sloppy Y-axis.
Try running the Test on the Chuck. The Chuck should make one complete rotation, then reverse direction and end up where it started. If this doesn’t come out right then change your mm/rotation till it does. I take a magic marker and make a little mark on top of the rotating part of the chuck so i know where it started.
Yes when I push test on the rotary set up page I get 1 full rotation 390*. I have also created a 4 inch line in lightburn and had the rotary engrave it. The rotary produced a perfect 4 inch line
Yes I am turning the rotary off.
I am powering the machine off.
OP’s setup shows chuck.
I spaced out that there are no splits in grbl laser rotaries until looking at OP’s rotary setup window and thinking it through. So what I thought what looked like a split issue is something else. Hopefully someone else can be of more help.
Following Along! 
Your line interval is too high. Try your line interval at .0064.
And also try turning on your cross hatch
