Confirmed possible 1.6.3 to fix this issue, so we know it's high on the radar right now: https://twitter.com/Dinnerbone/status/377820228815949824
Th3F4114n0n3 : Thanks for the Mojang Confirmation.
Pascal: Not a problem, seems I came of a bit harsh myself when responding.
Anthony Thyssen, Louis A. Nani, and Marius D: It seems Kabo (From the ZipKrowd server), has been messing around in the game code and has "fixed" the issue it seems. Waiting to hear back from someone to see that it work/Mojang's going to implement it.
Source: https://twitter.com/docm77/status/375876176297738241
Pascal : I've heard from various sources (none of which have Mojang confirmation from what I understand) that a fix was being deployed in 1.7 to not break existing structures. I was just passing along the information that it has indeed NOT been fixed at this time.
John W Bjerk: I haven't checked that as of right now.
Confirmed broken (again) in Snapshot 13w36a. Opened up a world save from 1.6.2 that contained a witch farm, witches were no longer spawning.
Bug still present in 13w06a (2nd version). Uploaded a short video to show the bug in action: http://www.youtube.com/watch?v=QkV7N9fp55Q
I've had the most success duplicating this bug in the North facing direction.
Tim: Did you load the chunks in 1.6.3 first, then change over to 13w37B? 1.6.3 adds the save mechanic, and 37B is the first one that will read it.,