Hey guys, sorry to revive this thread, but same thing happened to me and this is only topic describing exactly same problem I've found so far.

I already tried to delete all layers, then select a group that contains everything in my airship, create new group assigning selection. Then Visibility toggle works completely fine, but Template or Reference mode only changes parts of my model..

I also have sub-groups in my model, for example engines, wings,.. but it doesn't act on per-subgroup basis. For example my engines sub-group contains both the wing engines plus the back engine, but in template mode, only back engines changes.

I'm starting to loose my mind here.

Any ideas? I'm using Maya 2013 SP2 on PC.
Thank you very much for your time.