I have noticed the same issue and I think it is due to the workspace being built in the current (or non-existing when outside tmux) session instead of the new one.

I've found a bug in libtmux which is causing this, @romabysen is correct. So I will try to fix libtmux and it should magically fix tmuxp.

tmux-python/libtmux#65 has fixed this for me locally, so this should be fixed with the next version of libtmux.

@askedrelic if you're around, try seeing if pip install -U libtmux and trying to load a fresh session in tmuxp works.

tmuxp 1.3.2 is live

tmuxp 1.3.2 fixes this for me.

My use case for this has been restarting a tmuxp session, while I'm currently using it. I setup a bunch of ssh connections and restarting the whole session has always seemed like the easiest thing for me:

tmux-restart() {
    # kill client incase it exists
    tmux kill-session -t temp || TRUE
    # create detached session with commands
    tmux new-session -s temp -d 'sleep 1 && tmux kill-session -t dev && tmuxp load dev -y && tmux kill-session temp'
    tmux switch-client -t temp;
}

Indeed, tmuxp 1.3.2 seems to have fixed it. Thanks!