How did you install snort on FreeBSD? /etc/snort/* shouldn't exist.. It should be in /usr/local/etc/snort/*
I think you installed snort and prelude by hand.. Use the ports Luke!

cd /usr/ports/security/snort && make all install clean
cd /usr/port/security/prelude-lml && make all install clean
cd /usr/ports/security/prelude-manager && make all install clean

Everything should get fetched, build and installed in order, and more importantly, in the correct place..