I think I found the root of all my issues, I think there's an issue with playmaker and instantiating objects with colliders and rigidbody along with adding or removing rigidbodies at run time.
I have sent it as a bug report as when testing it in PM 1.4 it works. (before the trigger updates)
if everything is there at the beginning of the level, it all works fine, the issue I was (still) having is that the collision needed to be detected on instantiated objects and having a tone of issues due to the above.