Autofocus is not enabled yet AFAIK, and you can’t use anything thicker than about 0.5 inches on top of the crumb tray.
The laser needs a certain amount of distance to focus the lens … as you discovered.
If you want to engrave on something thicker than half an inch, you need to remove the crumb tray and prop the board up so that it falls into a certain range for the laser to be able to focus on it.
There’s a really good tutorial that @henryhbk did that shows how to do it here:
Sounds like you got lucky with the distance on your second shot though, so that was a good thing.
Sorry about that.