When creating a simple session like this:

session_name: test
start_directory: /tmp
windows:
- panes:
  -

It creates a window in the right directory but if I open a new window, it falls back on $HOME.
I don't have this behaviour with tmux new -s test -c /tmp.

tmux version: 2.6
tmuxp version: 1.4.2
libtmux version: 0.8.0
tmuxp and its dependencies were installed via pip install --user (python2)