Are those entities created dynamically via script or placed in WED/ wmb levels?
You can use a command like "LEVEL" (or similar, I think in a *.wdl file with the same name as your main script.c) to make sure all entities included in those levels get published. I have something like that in my project where I create level names dynamically (like "level%d" with str_printf).

When you search the forum for publishing issues and the publish process in general you should get quite some results.