What I just went through for a friends pfsense firewall was a learning experience. I install fresh copy of 2.2.2 I think then he did all the updates but squid3 would not work in transparent mode.
I checked the permissions and the owners to my own copy that works for cache folder and PID file. Since he had errors for bad cache folders and couldn't fix with squid -z. after deleting all the squid cache folders and recreating and all that still not run..
Last thing I did is delete EVERY instance of SQUID on the system after fixing permissions and then installed squid3 again and it all works for him now.
My system is working squid3 and Antivirus and so is a brand new friends firewall .. squid can't beat me!
Don't give up and I will never fail I tell myself!