I think this is an update issue of the Finder and maybe with JarBundler
not requesting some sort of update on the Finder. However, it is not
restricted to JarBundler as I initially observed this using the Export
to Mac OS X Bundle facility within Eclipse.
That could well be the case.
I don't know about associated documents but perhaps you could try the
same procedure with one of your documents - it might just produce the
correct icon for that one document or you might be lucky.
It's not the icons for the documents I care about--the standard icons
for the relevant file types are all fine--it's the ability to drag and
drop the right files onto my app in the Finder. I also want to be able
to select my app as the default for various file types and "Open With"
my application.