Ok, to rule out Repetier as the culprit I opened them both in Simplify3D (which was developed completely independent of Repetier) and it shows basically the same thing. S3Ds gcode visualization is very good and exact so I trust it based on hundreds of prints I've done.
Here are the comparisons with 2 different angles shown:
http://i.imgur.com/HPlwjnn.jpg
http://i.imgur.com/xA89hKx.jpg
I have not printed this little test case (only my actual models, which have the same problem), but in either case I would probably need a good macro lens as its hard to show in photos what the eye can see easily. Plus, I don't want the discussion to detract into possible physical printer issues (i.e., if I had shown the actual prints first, people may blame settings, z-wobble, etc).