OK, so I'm off to meet Karliah after getting the journal translated (Done this before on another character, so I know the routine) - I fast travel to the back door like I did last time...and the well entrance is locked! It wasn't last time, and I've never needed a key before to get in that way!

Did they do a patch that locks the back door on you in some circumstances?

It's supposed to be locked for that particular part of the quest. It's a one time event, and will always open for you after you've met Karliah (use the Ratway to get there)

^This. You have to go the long way this one time.