I have the exact same problem, I was about to make a post about this but I have just seen this one.
Its actually very annoying that it occurs I want to populate a entire region but I havnt got the motivation if its going to look so silly.
My region is all medium tiles aswell but I notice it happens on ready made regions too so its not to do with that. I too noticed that its in a checkerboard pattern.
I do not really see a reason why the game would be made to do it on purpose.