I'm pretty much stumped, but I will admit that from all your postings on this thread so far, I don't feel that you've explained yourself well enough for me to be sure I understand.
You mention squares, & you mention 12 x 12-1/16 ...but then you draw us a row of rectangles.
You also mention 5 good ones out of 10... then you draw the rows of yellow rectangles with all kinds of numbers of good, then bad. What do they represent... 3 different runs of different sizes?
The only thing closeto similar that I ever encountered was when I had a bunch of rows of decals that looked evenly spaced... but based on the fact that I had done "step & repeat" on some, & manually dragged copies into place on others... they were not exactly even... just very close. Anyway, I loaded a few sequences into the cutter backwards, & since they were almost equally spaced... the cutter started looking like it was perfectly aligned, but later, it went off. It confounded me for awhile, but in the end, the cuts weren't "going off" ...they were going exactly where I programed to go... that just happened to be wrong because i screwed up.
I would troubleshoot that issue by trying various components of your scenario isloated from other ones... like same art, copied into new file.
different art, with step & repeat done the same way
same art, different step and repeat.