Well, I just opened the project, and that script aliases Scene_Save, but that part is not running at all. That means the most likely explanation is that there are cmpatibility issues between scripts. Beyond that, I have no idea where you have hidden all the default Scene_ classes. I assume they're all tucked away somewhere in that mess of Custom Scripts. I also do not know why the scripter completely overwrites Game_Party, and then proceeds to do the stuff in Scene_Save, Scene_Load, since they are just loading instance variables of Game_Party. Regardless, the problem is probably incompatibility between scripts, not a problem with Marshal. It is not impossible to fix, but it is going to be a pain with all the custom scripts you have.
I might take a closer look if I have the time to, but for now I'm going to leave you with a question: What scripts have you added recently. I.e. what scripts have you added since the last known stable version of your game?
Also, WcW, I imagine the problem are the save games in those two projects. If you delete them, then I imagine your projects ought to work fine. Though, I couldn't know unless I saw it.