Through a little experimenting, it appears to have something to do with the wireless daemons running.
So, I've made a little VPN start-up script to reset everything.
So far, it appears to work 100%, woohoo!
sudo /etc/init.d/waproamd stop
sudo /etc/init.d/wifi-radar stop
sudo /etc/init.d/wpa-ifupdown stop
sudo /etc/init.d/xsupplicant stop
sudo vpnclient connect MyKey.pcf user myUserName pwd myPassword