There is a problem with your screenshot. Please embed it using the toolbar or drag it to the reply field on the forum. The Drag and Drop here tool is pretty useless.
Make sure you show us the modified properties of the layers that are giving you problems by selecting them and pressing 'uu' to show us what you have changed.
Try soloing layers until you isolate the problem of the black boxes.
When you are having problems with templates it is very helpful to have links to the templates. If there are a bunch of pre-comps or nested comps in the main comp it is also very helpful to see a flowchart. The flowchart view is also very helpful in diagnosing your own problems.