Did you make sure you clicked 'Update Z Order' before updating the areas? This allows Tunnel to calculate which areas should appear on top of others.
Failing that, are the areas which are not appearing in the correct order connected to centrelines through the overlapping passages? If not then sometimes the overlap comes out wrong, but you can set a vertical offset using connective lines to force one area on top of another. I'd have to dig out the details to tell you exactly how though.