What's causing these checker board-like machining marks ?

As you say, these marks aren't much of a big deal, but using the cutter you have on a small mill with the inserts you have will always produce these marks.

On small mills, you have to take care to not use inserts with too much rake. This will pull your cutter down into the work, unevenly. Even on my really big mill (3,800lbs) using a surface mill over 2" in diameter can result in this finish if I don't change out my inserts. Most of the time I finish aluminum with a HSS fly cutter with a 3-4 degree rake, with a 7 degree clearance angle. The nose radius is large, around 50 thou or bigger.

I hope this helps.
 
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