Is there a particular reason you have chosen XML config files? I have done XML configs in the past, and they have often turned out to be more of a headache than anything else.
I guess the real question is whether using something like the Preferences API might work better in your situation.
Reasons to use the Preferences API over a roll-your-own XML solution:
Avoids typical XML ugliness (DocumentFactory, etc), along with avoiding 3rd party libraries to provide the XML backend
Built in support for default values (no special handling required for missing/corrupt/invalid entries)
No need to sanitize values for XML storage (CDATA wrapping, etc)
Guaranteed status of the backing store (no need to constantly write XML out to disk)
Backing store is configurable (file on disk, LDAP, etc.)
Multi-threaded access to all preferences for free