Hi Pawel,
Changes made in the Configurations tab are not written back to the repository in 5.4. In 5.5 and later, they are written back to the repository, but to OSGi configuration nodes, not into /etc/map (or whatever location you have configured).
Can you point to where it is documented that configuration changes are written back to /etc/map? I'd like to file an internal documentation bug about that.
Regards,
Justin