I think that's a tooling glitch, which is unfortunately hard to reproduce, but can be worked around by appropriate Eclipse "dances" such as using "clean..." against the server to clear out the staging area, closing/opening the project, undeploying then redeploying, and ensuring the server is started with the clean option to be on the safe side.
If you can reproduce this predictably, please provide steps to reproduce and kindly raise a bug against the tooling. You can use the Virgo bugzilla as we probably won't be able to fix the bug before the tooling is contributed to Eclipse.
Thanks for your reply. After quite some toying around I think I found the (or at leas a) problem:
The main catch seems to be that previously I had Virgo installed outside of my home dir (/var/tmp).
After reinstalling it in my home dir I still had to perform your suggested "dances" for some bundles (others worked right away). But now everything looks fine.
I will check bugzilla if this is a known problem and create a bugreport if it is not.