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Ok, let's take a look at this;
No, that is most likely the new parts, or dust, metal shavings, and so on that he cleaned and serviced.
The metal is expanding and contrasting. After a little while the burner will become seasoned in a matter of speaking, and stop.
And if it is the dirt and dust, same thing, after it runs a while it should stop.
Some may even be coming from the ducts, since your heater was working only half of the burners, then it is running and producing more heat now
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Yes this would be my thought.
If he pulled the blower, and gave it a very through cleaning, it is very possible that he cleaned the burner, if he did, even tho he vacuumed it, there would be dust and metal pieces shavings and Burrs, that would pop like popcorn for a while.
If you do have a real concern you may want to have him inspect it one more time, just to set your fears to rest.
But based on what you are describing I would say you are ok.