How about they messed it up when they painted it. Maybe they painted it when it was wet.
But you said it was dry.
HMMM, the answer will be interesting.
Nope.
David Macy’s guess in post #15 is close, but not close enough to win.
Read my post #8 again.
The yard mixed the embossed wood-grain with the smooth.
Nope. Good guess though.
They are all wood grain on one side.
Cement Board trim is made with cementious products and due to the weight of trim boards, it is manufactured with a low density composite compared to the siding.
Having a low density, it is more apt to absorb moisute from humidity or plan bad handling and storage. Some small variation in thickness will occur. 
Different lots from Hardie?
MFG. Tolerances are with in 1/8 and the lumber yard mixed the different lots.
This “variation” is a nightmare as it the middle thickness boards land right between the 4/4 and the 5/4. Sometimes the trim carpenter mistakenly picks up the middle thickness trim when he meant to pick up the 4/4 and sometimes he mistakenly picks up the middle thickness trim when he meant to pick up the 5/4.
Did not use correct paint, used an oil based instead of a high quality acrylic.
Prussell’s guess in post #27 is getting really close, but not yet there.
It is something the lumber yard is doing that is causing the nightmare for their customers.
Up it to three bars to be donated to a charity of your choice.
And it has to do with rotating stock.
David Macy can’t take it any longer. LOL
Use the plastic wrapper that is provided to keep the product dry.
Prefinished siding must be kept covered with the bonnet provided and
kept dry at all times.
You got that right my friend. Do I hear 4 bars.
Alright, prize is now 3 bars of pure silver.
Sounds like someone, the lumber yard or Hardie, didn’t properly account for a saw kerf.
Nope.
Another hint: The counter at the lumber yard was perplexed. I had to go out and talk to the workers in the yard. They were the ones who explained that they rotate their stock of cement fiber board trim as it comes in. That’s how I figured out what was going on.