The issue is scene independent, i get the same horrendous saving times in all scenes, it only depends on the file size.
It's funny that you mentioned the prune scene, because the last thing that i did before i noticed this issue for the first time, was cleaning a scene with this script (i have the latest version). Right after i did this, saving time skyrocketed in the same scene and in the same max session. Don't know if it's related, or just pure coincidence.