I'm having the problem that if I use a Java-based implementation to unzip the src.zip (like the <unzip> task in Ant or the Jar command from the my JDK install) then javadoc ignores it. I have to use a tool like the unzip executable usually provided by the system on Linux machines. I can't find any difference in the contents of the produced directory trees, I even synched the permissions on the two trees. I posted a thread with an example source file and ant build file on the Ant developers list, see the link below.
The problem with this is, of course, that I have to have a non-portable solution to generating javadocs, and it only works on Linux because I can't assume the developer has installed a command-line unzip utility on their Windows machine.