The lines https://github.com/holman/dotfiles/blob/master/zsh/config.zsh#L18 and https://github.com/holman/dotfiles/blob/master/zsh/config.zsh#L26 seem to specify incompatible options. The second line also repeats SHARE_HISTORY.
From The Z Shell Manual:
SHARE_HISTORY <K>
This option both imports new commands from the history file, and also causes your typed commands to be appended to the history file (the latter is like specifying INC_APPEND_HISTORY, which should be turned off if this option is in effect).