Ran into an SMP glitch which messes up the spawn rates the longer the server is up. Resetting the server doesn’t seem to help it either. After some tinkering I realized I could fix it by setting the server to peaceful then back to normal. As soon as I did that I had tons of pigmen in the machine within seconds.
This could easily explain why sometimes we rarely see any spawns roaming around at night. It could also be the issue with the witch farm. Jared went into the blaze spawn area and ran into tons of mobs (15 or so) on one of the spawning pads. Hopefully this makes it easier to hunt down wither skeletons as well.