I have this problem with normals. It looks like Maya doesn't know which way they're pointing. I have two planes with bump textures and in viewport it looks like they're facing the same way but when rendered they are not. Well ... if I use SW renderer (mental ray/Maya Software) then they are not facing the same way but when I use HW renderer (Maya Hardware/Maya Harware 2.0) or when I just look at it in Viewport (and check with default matrerial and Two Sided Lighting off) then they are. Both of those planes have deleted history and freezed transformation. I think the problem is tied up with negative scaling (one of those planes is mirored copy of the other). Strange thing is that boolean operations agree with SW renderers. When I try to cut a hole in a plate with a negatively scaled cylinder then I have to use an Intersection instead of a Difference. That means that the tool thinks that the cylinder is inside out but i can clearly see in Viewport that it's not. This problem has occured to me on my laptop with Maya 2015 and now on my desktop with Maya 2016.