Maya 2008 P05 x64 on Linux.
This is an unusual one I've never seen before and I have a workaround, but it would be cool to find out why it's happening in the first place.
I have been running into issues with objects not obeying display layers unless I add the shape node as well. Normally, if you add the transform node to a display layer, the shape node automatically takes on the display characteristics of its parent transform node. This is occasionally not happening and on the surface everything looks correct.
I've checked the attrs of shape nodes that do this and they appear identical to shape nodes that behave correctly.
The fix I've found is to add the transform node to the layer (the normal way to do it), then pickwalk down to the shape node and add that to the layer as well. If I then load the input connections of these shape nodes into hypershade, I can delete the connections to that layer and the objects behave correctly again. One thing to note is if I just remove the shape nodes from the layer, they do not behave correctly. I don't want to leave the shape nodes added to the layer because this can cause problems later down the line if I need to reorganize my scene at all.
I don't know where this weirdness is coming from, but most of the time I think this is happening from objects imported from Rhino files, so I'm guessing there's some hidden attribute added to these objects upon import, but I haven't been able to find anything.
At least I have a workaround, but I'd like to know if there's a way to kill the problem from the start or if it's just some odd bug.
Thanks