Coordinate systems mating using Mate References flips axes

Question asked by Lennart Floreby on Feb 1, 2016
Latest reply on Sep 15, 2017 by Lennart Floreby

Why does Coordinate Systems mating behave differently if they are mated manually vs with Mate References?
What I mean is this: In both cases (manually and with Mate References including Align Axes), the coordinate system points will coincide, the X axes are parallell between the parts, the Y axes are parallell etc. BUT sometimes when mating using Mate References, two of the axes are reversed between the two coordinate systems. This never happens when mating two coordinate systems manually. I find this very strange. It seems "Align axes" means different things when mating manually (Coincide and align axes +X = +X,  +Y = +Y etc), and mating using Mate References (Coincide and align axes X = +/- X, Y = +/- Y, etc). Could you please explain this?

Additional informaiton: I am using SolidWorks 2014. The problematic Mate Reference do have a Secondary Reference Entity in the form of a Face that must be anti-aligned with the corresponding face in the other part, which in the problematic case is another instance of the same part! The Coordinate system lies within the plane (the secondary referece). The point of having the Secondary Reference, is to make it impossible to mate this part to itself, since the coordinate system mating is one way, and the face-to-face mating is anti-aligned. But the mating works anyway, which hinders the correct matings, which are to other parts. I am sorry if this is confusing.

I would be grateful for any input on this. Thank you!