I finally found some time to address this problem. It is indeed related to the fact that the new number gets assigned when you click on 'New'. So if two people edit the new entries at the same time, they get assigned the same number. To fix this problem, I made the tag generation work with the 'Subst' command, which is evaluated at the entry submission, and not when you click on 'New'. So to make this work, you need to upgrade to SVN revision 2152 and then put into your configuration file: 

Attributes = Author, RFC, Subject
Preset RFC = <will be assigned when you submit>
Preset on duplicate RFC = <will be assigned when you submit>
Locked attributes = RFC  Subst RFC = RFC-######

I also changed the documentation accordingly.