Without seeing pictures of your results, it’s hard to judge whether they are within tolerances considered normal. As you correctly suspect, it is possible occasionally to have a slightly warped piece of material that does not cut through all the way in a place or two. (Pinning it down flat helps, and the slightest amount of warp is going to affect it, so I tend to always pin using these: Honeycomb Pins)
Another thing that affects certain people is swelling from humidity…if you live in a high humidity area, you might find that slowing the cut speed down by 5 or 10 points will enable you to cut through materials like draftboard in one pass, whereas otherwise it’s going to take two. Glowforge has the ability to save Custom Settings so that it’s not any harder to use than the default. (That’s been a lifesaver for me… draftboard swells badly here.)
If you don’t want to do that, sending a second Cut operation without moving the material on the bed or the design on the screen will complete the cut. Before you do that, you will want to set any other operations such as Engraves and Scores to Ignore in the thumbnail column, or it will absolutely cut through parts you don’t want cut.
Sounds like you have a pretty good handle on it already though, especially after less than a week. Give the Custom Settings a try - you might like them. 