I’m cutting multiple pieces of the same art on a single board. The goal is to glue the pieces together to get a double or even triple thickness. The problem is that when I glue them up some of the layers aren’t the same. The differences are ever so slightly different, but more than what I can live with!
Anyone have a similar experience or have suggestions on what I’m doing wrong?
TIA
There is always a slight slant to the profile of the cut - it’s caused because the laser beam does not cut straight down through the wood, the power varies the farther away from the focal point. So more material gets burned away near the focal point. Thicker materials show it more than thinner materials.
Generally it’s close enough, but you can always sand it a bit and make it perfectly flush. Or use an adhesive band of veneer around the outside edges.
Sounds like your gantry is not square.
Cut a square, then remove, rotate 90 degrees, and put back into the cut area.
If it’s not a perfect fit, follow the support info on squaring up the gantry.
It’s really kind of hard to say without photos / artwork to look at. If the differences are like in the .004" range, @Jules’ answer is correct, but I don’t know if that’s what you mean by “ever so slightly.” 
Check your artwork to make sure nothing got accidentally skewed when you were arranging things in the GF interface. And check the original to make sure it didn’t happen even earlier. That’s all I can think of without seeing a visual!
Also, happy cake day!
I’m so sorry to hear that you’re running into trouble. In order to help narrow down the snag, would it be possible to obtain some images of the results you are noticing when printing?
Once we can review the images, we’ll send over the next best steps.
It’s been a while since we’ve heard from you, so I’m going to close this post.
If you are still having trouble, please start a new post or reach out at support@glowforge.com. We’ll be happy to take a look.