We are using nagios and mysql in our fc6 system. We have used ndoutils addon to connect mysql and nagios. All the tables in mysql are updated with respect to the information from nagios except nagios_logentries table.
I have not setup Nagios with MySQL, so my advice (being a beginner as well) is limited.
Have you checked the permissions? That would be the first step in troubleshooting, if the DB isn’t updating. Make sure you can connect to the database with the associated user.