CraftBukkit 1.3.1 is still in development which means there will be bugs like these. Be patient for a Beta or Recommended Build. Also make sure to update your plugins if an update is available for them.
Also look at your chunks and entities they should never get that high. QUESTION: What version of java are you using?
I see everyone posting these. Its there a command I dont know about, or is that a plugin showing your TPS?