However, when I see problem items in the "Problems" view, and the error markers in the "Projects explorer" I don't see them in my navigator. Is there something I forgot to do? My custom navigator shows the same projects/files as the project explorer.
Look at the code to see how JDT does it (and look at the documentation for the problem markers) and do it that way for your instance of the CNF, or wait for the bug mentioned above to be fixed (which could be a long wait).
Off the top of my head, I don't know anything about how problem markers work, so that's the best I can offer you.