This is why nrpe writes its pidfile in /var/run/nagios by default.

On a clean 10.04 install:
---
root@cacti01:~# grep ^PIDDIR /etc/init.d/nagios-nrpe-server 
PIDDIR=/var/run/nagios

root@cacti01:~# grep pid /etc/nagios/nrpe.cfg 
pid_file=/var/run/nagios/nrpe.pid

root@cacti01:~# grep nrpe_user /etc/nagios/nrpe.cfg 
nrpe_user=nagios

root@cacti01:~# ls -lh /var/run/ | grep nagios
drwxr-xr-x 2 nagios root 4.0K 2011-11-25 17:24 nagios

root@cacti01:~# lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description:    Ubuntu 10.04.3 LTS
Release:        10.04
Codename:       lucid
---

Could it be that you upgraded without properly updating your nrpe.cfg?

The above is up to date lucid, if I remember correctly, both the default
nrpe.cfg and default init script are identical in 11.10 but I may be
wrong, if I'm, then Sander-oele's bug is still valid.

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https://bugs.launchpad.net/bugs/883904

Title:
  nit.d script incorrectly assumes PID file --> can't stop service

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