I had this problem because I was using tmux-next.
Initially I solved it just by passing the config file explicitly tmux -f ~/.tmux.conf as the question here points out. (I had already aliased tmux-next to tmux.)
Then I realised tmux-next is using tmux-next.conf, so just symlink it if using this and only need to run the next tmux version.
ln -s ~/.tmux.conf ~/.tmux-next.conf