If i have a tool with polypaint already applied, then create a layer to sculpt or paint on, then hide part of my model using group selection the original polypaint gets fractured/pixelated/total chaos over the tool.
This happens even with the default polyshere.
example:
I’m afraid that layers are problematic, particularly for polypaint. You might find this thread has some useful information:
http://www.zbrushcentral.com/showthread.php?166033-3D-layer-bugs