I have this issue in both 2012 and in 2013.
Anything structural that is inserted into the model if "off" by a bit.
try drawing a line, then create a member from this line. zoom in and you will see how it is "off"
This casues major issues and problems. If you dont catch this right away it will domino effect all the way through your structure and you will end up with one screwed up model.
When you click on the Member Settings are the offsets for the Member set to 0?