As of apache 2.0.52-r3 and 1.3.33-r1 apache's configuration locations have changed. nagios-core currently has paths hardcoded. by inheriting depend.apache you can use predefined variables in the eclass to install your configuration files in the correct locations. Thanks!
nagios-core-1.2-r4 - apache people - can you do a quick check to see if I've covered everything please.
fixed -thanks Michael.