Bison latest version installed but not in use

I just ran into the same issue - in my case brew wasn't creating the symlinks. You can force this in order to get the right version via:

$ brew unlink bison
Unlinking /usr/local/Cellar/bison/3.0.4... 0 symlinks removed

$ brew link bison
Warning: bison is keg-only and must be linked with --force
Note that doing so can interfere with building software.

$ brew link bison --force
Linking /usr/local/Cellar/bison/3.0.4... 9 symlinks created

$ source ~/.bash_profile
$ bison -V
bison (GNU Bison) 3.0.4

$ brew unlink bison
Unlinking /usr/local/Cellar/bison/3.4... 0 symlinks removed

$ brew install bison

$ brew link bison --force
Linking /usr/local/Cellar/bison/3.4... 9 symlinks created

$ echo 'export PATH="/usr/local/opt/bison/bin:$PATH"' >> ~/.bash_profile

$ export LDFLAGS="-L/usr/local/opt/bison/lib"

$ source ~/.bash_profile
$ bison -V
bison (GNU Bison) 3.4

You have /opt/local/bin in your path before /usr/local/bin. Homebrew installs in /usr/local/bin by default so maybe you have another version in /opt/local/bin that gets found first.