James Ward

To easily replicate this bug, a set-up similar to the one in the attached screenshot is advised.

So, Searge. you're telling us that ONLY witch huts within your new "fixed" bounding box spawn witches, meaning if we find a hut that is higher of the ground than normal, we can't convert it into a farm. THIS ISN'T A FIX. After having spent 10's of hours spawn-proofing my perimeter to have my farm "fixed" to only have one working floor is more than a disappointment, to say the least.

However, it is interesting to note that on THIS ["Witch Farm"] world, originally supplied by Redstone Spire, wherein the spawning pads are located at y=64 and y=68, ONLY witches spawn on BOTH floors in 1.7.10 AND in 1.8.

I hope that my resources can be utilized to find a solution to this issue.

The attached "example world" can be switched from 1.7.10 to 1.8 and back to demonstrate the bugged spawning behavior explored in the above screenshots. Searge, hopefully, this can be used to assist you to figure out the problem and resolve this issue.
NOTE: The perimeter was made in less than 5 minutes in MCEdit and is hence, no where near perfect. To get mobs to spawn, one might have to switch from hard to peaceful and back again.

1.8; identical situation to previous screenshot - same world, same conditions. Pads are located at y=67 and y=71, however, all hostiles can spawn on the top pad while witches only spawn on the bottom pad.

EDIT: changed y=68 to y=67

1.7.10; spawning pads at y=67 and y=71 in swampland M. Witches spawn on both pads, no other hostiles spawn on these pads.

EDIT: changed y=68 to y=67

In 1.8 Pre-3 My witch farm (from 1.7.10 directly) (originally generated in 1.7.4) spawns non-witches on the uppermost floor (at y=71, lower is at y=67 - Swampland M), suggesting that this issue remains unfixed.