Thanks for the clarification. Just a guess here, but I'm guessing you had snort installed somewhere before June3rd or so.
Going through that process on a new install of RC3, and repeating your process:
Jun 30 09:05:57 SnortStartup[36413]: Snort HARD Reload For 45292_re1…
Jun 30 09:05:57 SnortStartup[33404]: Snort Startup files Sync…
So with SNORT loaded, reset, interface reset, pfsense updated to latest snapshot, rules downloaded again, updated, and a few rules selected to filter...no go. Based on the removal of the 32 bit snort package, I'd guess there are known issues with the 64bit version too that are not being shared here.
Cheers,
D.