I've got a few wither skeleton grinders in the regular SMP3 nether, the most recent one having been built just before the 1.6 upgrade at x=9999, z=9999. Wither skeletons almost never spawn anymore, and haven't since the 1.6 upgrade. I read that the problem was understood by the support team and that they were returning the various nether maps to their original seed values, or something like that. However, I still haven't seen any improvement in wither skeleton spawning at any of my grinders in the nether. Can you investigate?
I contacted Aikar about this about a month ago. He thinks he has a solution, but said he won't be able to work on it until after he is finished with the 1.7 update.
I went ahead and removed the coords from my original post, although I've built it to be a public grinder for any of the folks on SMP3.