OSX 10.11.6, Windows 10, Ubuntu Linux 17.10
Broken: all actual builds 2.79.1 (GPU and CPU tested)
This is a hard one to describe and there are other pass combinations which trigger the effect.
Two render layers (RL) with different passes selected (if only one RL is active it works as expected)
RL1 with Combined and AO pass, RL2 also with Combined and AO pass - all is fine.
RL1 with Combined, AO, Normal and DiffuseColor pass, RL2 same as above - broken
Activating Normal and DiffuseColor pass in RL1 seems to break RL2 somehow.
I added some images and .blend file for further testing.