I'm having a very similar problem since upgrading to 4.0. I have a significant amount of development work working under 3.2.4/6, and I thought it was time to upgrade. Now, none of my archives seem to be part of the classpath. The only applicable note I've found so far was on the Wiki which says something like, "the classloader scheme has changed in 4.0, try running the 'standard' server implementation for something closer to 3.2.x." I deployed my stuff to standard and ran it, and, sure enough, everything worked fine.
I've tried several different solutions, including the manifest classpaths that you mentioned, but with no luck. If nothing else, I think the 4.0 administrators guide is supposed to be released soon.
Wish I could be more help,