I've mentioned this in a post in the feature request forum, but seeing as it may get lost as a possible bug in there, I thought I'd create a thread for it here.
I've also submitted a bug report for it.
When rotating a layer with a 3D Box on it, the 3D Box doesn't not behave as it should.
To reproduce it, place a few sprites on a layer, place a 3D Box next to them, and then rotate the layer.
To me, it looks like it's either using another co-ordinate system, or it's just not being associated with the layer in the rotation code.