I have a total of 3 saves in my saves folder as I thought I originally had too many since my initial play-through a year ago was still in there.

I've escaped from the dungeons 3 times now. I save (quick or manual doesn't matter), I quit or what have you, and every time.... EVERY. TIME. I end up standing by Foltest in the courtyard after opening the monestary gate. I don't know why Auto-Save or saving in general suddenly shut off, but it did.

I'm starting to run out of patience, I really am. There is only soo often you can repeat the same hour of gameplay.

EDIT:
This is all following a fresh install. I thought that maybe my game had corrupted, so I reacquired it from Steam.

Anyone got any suggestions?

I have the SAME issue, or had. I love this game to death, but seriously, the patch broke it more than fixed I think. I redid a part later in the game and wasted about the same amount of my time as you. The quickest thing to try is to just delete all of your saves except your most recent saves. Its an issue with steam cloud. really annoying, but its there. Exit the game, go and manually delete all of your saves except the same one you didn't delete in game. This worked for me, however, now I am having issues getting the game to save onto my damn HDD now. I still can play no issues, cause it saves in the cloud, but I have to always keep deleting old saves and just keep a few open. should work, other people in different forums had same issue as us. and this worked for them too. the cloud gets confused and stops it from saving entirely once is gets full, don't let your steam cloud get full for witcher 2 is basic thing now.