It maybe down to the following.
When Yosemite was released i.e. OS X 10.10 and therefore the version before the current El Capitan version, Apple changed things so that if a server has both SMB and AFP available then the Mac will default to using SMB to connect to the server. El Capitan will therefore like Yosemite default to using SMB in preference over AFP.
However there should still be a way to connect specifically using AFP or specifically using SMB regardless of this. You are probably connecting to the FreeNAS server by seeing it listed in the Sidebar in the Finder, i.e. in the left of a Window. This method will default to SMB, as will the browse network option. (Go Network from the Go menu.)
If you however (in the Finder) select 'Connect to Server' from the Go menu and type in an address like this
afp://name-of-server.domain.com
or
afp://name-of-server.local
or
afp://192.168.1.10
They should all force an AFP connection, likewise the following would all force an SMB connection.
smb://name-of-server.domain.com
or
smb://name-of-server.local
or
smb://192.168.1.10