I just updated the server to Pixelmon 3.2.9, so make sure to update your clients so you can play.
I'm also adding the SpawnOfPsyduck mod, so that I can control spawns a bit better. I plan to possibly do some tweaking with this in the future, and am open to suggestions regarding it if any of you have knowledge regarding it.
Here is a list of key/important features that come with 3.2.9(From the changelog):
The full list can be found here: http://pixelmonmod.com/changelog?id=31