I ran into this problem, when exporting a model to Sketchup. I have two separate layers, with sublayers for different materials for components.
When I export this to Sketchup, only the second set is put to right layers, and the other set is placed in full to “Layer0”.
I was able to replicate this with a simpler model, using identical sublayer names.
I am using Rhino 5 for Windows (Version 5 SR12 64-bit (5.12.50810.13095, 8/10/2015)) and Sketchup Make 15.3.
Sketchup export plöugin version (Aug 10 2015 15:14:46)