Another thing that's worth noting, the Skull Collectors don't trade the skulls for Blazes, Cave Spiders, Regularass Spiders, Ghasts, Magma Cubes and Pigmen. Villagers are really finicky with NBT data for items they trade, so I'm guessing something changed between the making the villagers and making the mobs that drop skulls. The standard skulls (Zombie, Skeleton and Wither Skeleton) all work fine though.
Yeah, I noticed that when I played through today. My guess is that the custom player heads that drop from mobs are getting a new UUID but, I haven't checked that out yet. If you mine the custom heads that are around the obelisks, those still trade.