I am having the exact same problem with a fresh install of 9.04.
Everything worked fine for me with 8.04.3...

I have 2 NICs - one facing the world and one for embedded linux
development - eth1

I installed dhcp3-server

So I have configured eth1 as:
mar...@adserver2:/var/run$ ifconfig eth1
eth1      Link encap:Ethernet  HWaddr 00:01:03:dd:97:fd  
          inet addr:10.0.0.1  Bcast:10.255.255.255  Mask:255.0.0.0
          inet6 addr: fe80::201:3ff:fedd:97fd/64 Scope:Link
          UP BROADCAST RUNNING MULTICAST  MTU:1500  Metric:1
          RX packets:0 errors:0 dropped:0 overruns:0 frame:0
          TX packets:56 errors:0 dropped:0 overruns:0 carrier:0
          collisions:0 txqueuelen:1000 
          RX bytes:0 (0.0 B)  TX bytes:9624 (9.6 KB)
          Interrupt:22 Base address:0xef80 

Next, I edited the file /etc/dhcp3/dhcpd.conf and added this at the end:

subnet 10.0.0.0 netmask 255.0.0.0 {
range 10.0.0.20 10.0.0.30;
host tsboard{
}
}

In 8.04, the command:
sudo dhcpd3 -d eth1 would then bring up dhcp on that interface and all was good.

In 9.04, the same command results in:
mar...@adserver2:/var/run$ sudo dhcpd3 -d eth1
[sudo] password for martin: 
Internet Systems Consortium DHCP Server V3.1.1
Copyright 2004-2008 Internet Systems Consortium.
All rights reserved.
For info, please visit http://www.isc.org/sw/dhcp/
WARNING: Host declarations are global.  They are not limited to the scope you 
declared them in.
Wrote 0 deleted host decls to leases file.
Wrote 0 new dynamic host decls to leases file.
Wrote 0 leases to leases file.
Listening on LPF/eth1/00:01:03:dd:97:fd/10/8
Sending on   LPF/eth1/00:01:03:dd:97:fd/10/8
Sending on   Socket/fallback/fallback-net
Can't create PID file /var/run/dhcpd.pid: Permission denied.

I have absolutely no idea what to do...

Any thoughts?  Thanks.
Martin.

-- 
(Dapper, Hardy) can't create /var/lib/dhcp3/dhclient.eth0.leases: Permission 
denied
https://bugs.launchpad.net/bugs/39249
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