Ok everyone, here's my current situation.
Two weeks ago, my PS3 Slim began to eat the top of my discs, so much so that eventually the games would not run and the console would stop working completely. Thankfully, I thought to myself, I have PS Plus with auto upload, so that my data would be backed up on the Cloud even though my slim has died (may her soul rest peacefully). But JUST TO BE SURE, I selected the "copy all" feature to the cloud in my Slim's twilight hours to be one hundred percent sure that my saves (about 500 mb worth) would make the transition to my new super slim intact. Hell, I did it twice.
And, OF COURSE, when I finish setting up my new system and settle down and upload my saves, I am astonished (horrified) by the fact that there are specific save files missing altogether. My Uncharted 2, Assassin's Creed II, Crysis 2 and many more files apparently did not make the transition over to the Cloud, even though, oh, I don't know, I selected the copy ALL save file function on the system multiple times in the 7 months I've had the service.
Hilarious. And totally typical.
Am I screwed? Are these save files possibly "hidden" in the cloud somewhere or are they forever lost? Uncopyable saves (like AC2) are still allowed to be moved using PS Plus, so what the heck is the gosh darn deal here? Super **bleep**, and hope someone can help/has had this situation happen to them.
I think that you may also have misinterpreted what the automatic upload option for save data does. If you read the manual, you will note that it says that the save data for the game will be uploaded "regularly". That doesn't mean "every time it changes", or "immediately". If you want to make sure that the most recent save data is uploaded, then you have to do it manually. Also, the function only works if you have automatic updates enabled on that PS3, and each PSN account can only enable automatic updates on one PS3 at a time. Also, I'm not aware of an option that turns automatic upload on for all PS3 save data. Where did you find that?