To put QR codes on the mints, you should focus the beam in as sharp a spot as possible, and then just burn every black QR pixel. This should work far better than trying to burn squares.
Candy usually doesn't turn black when you laser it, it just vaporizes and melts and turns shiny, caramelizing a little, sort of like overheating sugar. Can't burn black into a mint. The laser point is actually very fine - about 1/1200 of an inch - but the only way to mark candy visibly is to crank up the power to the point it melts pits into the candy far deeper than 1/1200.
Also, we don't even have Trader Joe's here in Utah. Apparently they won't open up shop here because they don't like the restrictive liquor laws (or so it's been said). The mints were a gift from someone in Nevada, so I don't even have an easy supply of these particular nicely laserable mint boxes, assuming I was willing to spend half an hour per box of mints to engrave them one at a time. (Too bad no BiddingPond or else maybe I would auction off the single box =) )
they finally saw the light. 
