I have learned that the tiled importer in Cocos2D should not be used as is for complex layer based maps. I have ran into odd display issues (lines between layers) and odd limitations (one tilesheet per layer).
The work around I am going to attempt is to load strictly the data that I need using the TMX loader and build a map based on that data. Basically, the Tiled map editor will turn into a placeholder creator.
Once that work is complete, I may look into updating the TMX loader to be a bit more robust, given that I’ll be deep in its bowels soon.