Old problem with snort on my pfSense 1.2.3-RC installation.
When I have two gateways, especially one being IPv6, snort, of course, freaked out when trying to grab the gateways. I removed the IPv6 gateway and now snort is grabbing IPv4 + nothing, putting in a ",," into the home_net. I've been adding this line:
$home_net = str_replace(",,", ",", $home_net);
To fix the problem.
Ever since my first time using snort I've had this problem. I recently had trouble with whitelists until I did an uninstall & install. The old snort package (before 2.8.6) should be totally gone.