While your theory is not impossible, this sounds like a material issue. I am guessing it wasn’t completely flat or it wasn’t uniform (or both). What material was it? If it was a plywood you could easily have had an inconsistent middle layer. If it was a hardwood the thickness can vary especially at the end, depending on how it was planed.
It’s a hard to investigate after the fact but you can inspect plywood with a bright light, and use calipers to test thickness. As for warp that’ll be really hard to verify.
Support will have you test by thoroughly cleaning the optics (as per the instructions on the support section) and then printing a gift of good measure on draft board in the spot where you had trouble.
Plywood inspection:
https://community.glowforge.com/t/trick-for-inspecting-plywood/15168
Cleaning instructions:
https://glowforge.com/support/topic/troubleshooting/cut-didnt-go-through-material