Well, the summary pretty much sums it up. Nagios, at least 1.2, can use a mysql back-end for retention data. Only by sheer coincidence, does mysql start before nagios in most cases. However, at least on my machine, mysql will always shutdown before nagios, making the saving of retention data impossible. Adding mysql to use solves this. It could even be done via sed if USE=mysql, if so desired.
Fixed in cvs