When you go to save It will save once....but will not save again or over write and what more is that the only way to fix this god awful problem is to just manually clear save.....Apparently the way that the save function work in this creator is that Once you hit save It save your game state And by game state i mean every Javascript you had loaded to that save.
So even if you change up the whole thing that load will go back to the exact save spot and Javascripted. I know ive loaded and tried to move my character resave did nothing. And we do need a Clear save function. In some game it allow for clearing all old save files.