I’ve moved this to Beyond the Manual because staff can’t help you with non-PG materials.
The quick answer is, yes, there can be variation in materials - but also draftboard is the dirtiest material one can cut, and loss of cutting power is the first thing that happens when your optics get dirty! Go here for the “Things that need wiping” section: Cleaning – Glowforge
Also - are you using the honeycomb hold down pins? If no, print yourself a handful and use them on everything. They are a wonder of the 
world.