Nice confusing post. 
What I Do remember from my time when I was using steam cloud is, that when you disable cloud saving, in the GD or steam, the local save data will probably be used as default every time you load up the game.
If you haven´t used them in a while, they will be super old, and what you copy in the cloud save folder is irrelevent, because it simply won´t get used.
Are you sure cloud saving is enabled in steam adn the GD client?
Maybe this helps. Sorry for your trouble. What a mess. :o