I'm having this same problem on a FreeBSD 6.2 machine where occasionally, I'd get the "It appears you do not have permission" message. Clicking refresh a few times gets rid of it.
Prior to redoing all my cfgs from scratch, a similar problem occurred where I could only see the localhost and no the 15 hosts that I had setup.
I've tried stop as well as rebooting the machine without success.
The output from a ps -ax | grep nagios only shows one instance unless any of the check_plugins are running, in which case there are two (parent and child?).
[root] /var/spool/nagios>ps -ax | grep nagios
88181 ?? SsJ 0:00.81 /usr/local/bin/nagios -d /usr/local/etc/nagios/nagios.cfg
90425 p3 R+J 0:00.00 grep nagios
Any help would be greatly appreciated.