Ok then, this might not solved the problem, but you shouldn't start Jonas/libresource with the root user. Otherwise you will have problem with file security on your file system.
I supposed that your postgres is running under the postgres user ?
If so you might run libresource with that user or create a specific libresource one...
To come back on your problem with SVN.
When you list the content of the root SVN repository with the SVN command line what do you see ? (Sorry I don't have it in mind)
You sould be able to see the directory 56a69d087f000001000018752e6de017.
If not, this mean that the libresource didn't managed to commit this directory to the svn.