I am curious how folks have compensated for having an uneven burn on a project (particularly wood). It doesn’t seem un common for me to have a dark stripe somewhere in the engraving.
Without a picture it’s hard to say but in general, the natural changes in density due to variations in wood grain show thru engraving. There’s no workaround for that.
Many times this is the result of the natural variations in wood. Not much to be done except visually inspect the wood for obvious variations before the engrave.
The only solution I’ve found for this is to use a wood that doesn’t have such a pronounced grain. Oak for example had given me problems like you describe. I switched to alder. The grain is much lighter and engraves very evenly.
Or post process - before removing the masking, hit it with some Minwax Mission Oak Polyshades. This works great to give an even color for things where you’re not looking for shading (won’t work for photo engraves).
Engraving plywood often has nasty surprises in the lower layers