Altium Designer: mixed mechanical layers on Top and Bottom Layer Pair
You need to create a layer pair that links M1 to M13.

The procedure differs from which version of Altium you are using.
I can provide instruction for Altium 18 but anything before that, you might have to look in the layer settings.

The easiest way to reorient the components, is from within the footprint lib, update PCB. I had something similar happen recently and my colleague showed me that trick.