So i'm using Dev version 319, most settings are getting reset after every 1 or 2 launches, things such as auto-warp, auto-stage, ascend path in the ascend guidance, this are the only things i've noticed since are the ones that i use the most.

yea same for me. tho it seems rather strange when it does or doesn't remember settings. but i remember that MJ used to have different setting for each craft but i have not seen that working for months at least.

Probably a related problem under 2.4 build 341 :
Some windows* don't display at same position than previous mission.
(*) Manoeuver Planner/Editor and Warp Helper always appear at left top

It's seem MJ have settings for each vessels. That's could explain we believe it's a bug...

I submit default settings for new vessel re-use last drived vessel settings.

Windows position and config are sotred in the global config. It works fine for me.

Works fine for me too.
Chances are that you have a corrupted config and it chokes on that,
fails loading and simply defaults to nothing because of that. It already
did that often in the past.

If you could provide a log we could check if there's anything about that
in there.