Ever since SW has introduced the mirror components I have had 0 problems with it until now... Picture if you will a top view of a rectangular box, I am trying to mirror the right wall of the box to the left side, simple right? Well check this out
Step 1 select the right wall
Step 2 a preview of the wall being mirrored to the left side with RIGTH PLANE selected as my mirror plane (I don't typically need to reorient it, I am just in this step to show everyone a preview)
Step 3, What the heck went wrong? It shifted my whole wall by some odd ball number, approx 7/16" off
Test and Theories, here is what I have done
1. I have went back to make sure my assmblie and parts involved are all built on center planes
2. The default Reorient compoment option is "2 of 4" which basically flips the wall to the other side, the way I want. If i select 3 or 4 which turns my wall upside down it brings the wall to the front like it suppose too but however it will shift the wall 90% off to the right (using pic 3 as a reference)
3. If I chose option "1 of 4" my wall will be cenetered perfectly, but it is upside down which not a good solution for other reasons.
4. If edit this feature and I pick other components in my assembly they mirror perfectly.
I can't see what your wall looks like but from your description it sounds like it's not just a solid symmetrical piece. Thus the comment about it being upside down. So I think you are being bit by the mirror about the center of gravity method that is the current mirror method. You can test this by mirroring a plate, then changing the config of the mirrored part to one that has a hole in it off center. The part will move on some mirror orientations.
WT