The separate shoulder option has not worked for any of my characters since 10.2.6 with BetterWardrobe enabled. All of my characters that I log into are not presented with the second shoulder slot when checking the “transmog each shoulder separately” box. I’ve tested this on a class of each armor type.

When I disable BetterWardrobe this option finally works for me. I've checked other addons and none of them seem to cause the issue, only BetterWardrobe.

Should be fixed in next update