Still present in 9.10 after upgrading except now the VPN no longer seems to function and allow me to connect. All is the same at the other end of the VPN and I'm pretty sure it is configured the same as it always was in network manager at my end.

route before vpn:
Destination     Gateway         Genmask         Flags Metric Ref    Use Iface
192.168.1.0     *               255.255.255.0   U     2      0        0 eth1
default         router.home     0.0.0.0         UG    0      0        0 eth1

route after vpn:
Destination     Gateway         Genmask         Flags Metric Ref    Use Iface
oux6513-vpnouts router.home     255.255.255.255 UGH   0      0        0 eth1
192.168.1.0     *               255.255.255.0   U     2      0        0 eth1
138.251.5.0     *               255.255.255.0   U     0      0        0 tun0
138.251.0.0     *               255.255.0.0     U     0      0        0 tun0
default         *               0.0.0.0         U     0      0        0 tun0

Daemon.log:
Feb 21 00:30:45 chris-laptop NetworkManager: <info>  Starting VPN service 'org.freedesktop.NetworkManager.vpnc'...
Feb 21 00:30:45 chris-laptop NetworkManager: <info>  VPN service 'org.freedesktop.NetworkManager.vpnc' started (org.freedesktop.NetworkManager.vpnc), PID 3850
Feb 21 00:30:45 chris-laptop NetworkManager: <info>  VPN service 'org.freedesktop.NetworkManager.vpnc' just appeared, activating connections
Feb 21 00:30:45 chris-laptop NetworkManager: <info>  VPN plugin state changed: 1
Feb 21 00:30:49 chris-laptop NetworkManager: <info>  VPN plugin state changed: 3
Feb 21 00:30:49 chris-laptop NetworkManager: <info>  VPN connection 'St-Andrews Uni' (Connect) reply received.
Feb 21 00:30:49 chris-laptop NetworkManager:    SCPlugin-Ifupdown: devices added (path: /sys/devices/virtual/net/tun0, iface: tun0)
Feb 21 00:30:49 chris-laptop NetworkManager:    SCPlugin-Ifupdown: device added (path: /sys/devices/virtual/net/tun0, iface: tun0): no ifupdown configuration found.
Feb 21 00:30:50 chris-laptop NetworkManager: <info>  VPN connection 'St-Andrews Uni' (IP Config Get) reply received.
Feb 21 00:30:50 chris-laptop NetworkManager: <info>  VPN Gateway: 138.251.5.1
Feb 21 00:30:50 chris-laptop NetworkManager: <info>  Tunnel Device: tun0
Feb 21 00:30:50 chris-laptop NetworkManager: <info>  Internal IP4 Address: 138.251.5.80
Feb 21 00:30:50 chris-laptop NetworkManager: <info>  Internal IP4 Prefix: 24
Feb 21 00:30:50 chris-laptop NetworkManager: <info>  Internal IP4 Point-to-Point Address: 138.251.5.80
Feb 21 00:30:50 chris-laptop NetworkManager: <info>  Maximum Segment Size (MSS): 0
Feb 21 00:30:50 chris-laptop NetworkManager: <info>  Static Route: 138.251.0.0/16   Next Hop: 138.251.0.0
Feb 21 00:30:50 chris-laptop NetworkManager: last message repeated 9 times
Feb 21 00:30:50 chris-laptop NetworkManager: <info>  Internal IP4 DNS: 138.251.66.46
Feb 21 00:30:50 chris-laptop NetworkManager: <info>  Internal IP4 DNS: 138.251.40.10
Feb 21 00:30:50 chris-laptop NetworkManager: <info>  DNS Domain: '(none)'
Feb 21 00:30:50 chris-laptop NetworkManager: <info>  Login Banner:
Feb 21 00:30:50 chris-laptop NetworkManager: <info>  -----------------------------------------
Feb 21 00:30:50 chris-laptop NetworkManager: <info>  (null)
Feb 21 00:30:50 chris-laptop NetworkManager: <info>  -----------------------------------------
Feb 21 00:30:51 chris-laptop NetworkManager: <WARN>  nm_system_device_set_ip4_route(): Failed to set IPv4 route on 'tun0': Sucess#012
Feb 21 00:30:51 chris-laptop NetworkManager: last message repeated 8 times
Feb 21 00:30:51 chris-laptop NetworkManager: <info>  (tun0): writing resolv.conf to /sbin/resolvconf
Feb 21 00:30:54 chris-laptop vpnc[3862]: can't open pidfile /var/run/vpnc/pid for writing
Feb 21 00:30:55 chris-laptop NetworkManager: <info>  VPN connection 'St-Andrews Uni' (IP Config Get) complete.
Feb 21 00:30:55 chris-laptop NetworkManager: <info>  (tun0): writing resolv.conf to /sbin/resolvconf
Feb 21 00:30:55 chris-laptop NetworkManager: <info>  Policy set 'St-Andrews Uni' (tun0) as default for routing and DNS.
Feb 21 00:30:55 chris-laptop NetworkManager: <info>  VPN plugin state changed: 4
Feb 21 00:30:55 chris-laptop nm-dispatcher.action: Script '/etc/NetworkManager/dispatcher.d/01ifupdown' exited with error status 1.

ifconfig:
tun0      Link encap:UNSPEC  HWaddr 00-00-00-00-00-00-00-00-00-00-00-00-00-00-00-00  
          inet addr:138.251.5.80  P-t-P:138.251.5.80  Mask:255.255.255.0
          UP POINTOPOINT RUNNING NOARP MULTICAST  MTU:1412  Metric:1
          RX packets:35 errors:0 dropped:0 overruns:0 frame:0
          TX packets:78 errors:0 dropped:0 overruns:0 carrier:0
          collisions:0 txqueuelen:500 
          RX bytes:9331 (9.3 KB)  TX bytes:8909 (8.9 KB)

eth1      Link encap:Ethernet  HWaddr xx:xx:xx:xx:xx:xx  
          inet addr:192.168.1.2  Bcast:192.168.1.255  Mask:255.255.255.0
          inet6 addr: fe80::213:ceff:fe60:5a67/64 Scope:Link
          UP BROADCAST RUNNING MULTICAST  MTU:1500  Metric:1
          RX packets:11410 errors:0 dropped:0 overruns:0 frame:0
          TX packets:10727 errors:0 dropped:4 overruns:0 carrier:0
          collisions:0 txqueuelen:1000 
          RX bytes:7520776 (7.5 MB)  TX bytes:2233401 (2.2 MB)
          Interrupt:17 Base address:0xe000 Memory:dcffd000-dcffdfff 

/etc/resolv.conf:
nameserver 192.168.1.1
nameserver 138.251.66.46
nameserver 138.251.40.10
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