Planet Minecraft

Hello, I just updated my server to 1.3.1. I did this by replacing the old craftbukkit with the new version (thats how you do it right?). so I started the server, logged in, but when i was logged in all of the land/terrain was gone (there was no land). There was also monsters and mainly squids sometimes covered in black falling? So i waited a bit, flew around and big rectangles of land loaded but just in some spots, and monsters kept falling. I then disconnected from the server to see if the same thing would happen again, to my luck the same thing happened .I went to my friends house and asked him to go on the server. He went on and it was the same thing for him. Any ideas?
Im clueless, please help that would be great!!!!

Do you have any plugins on the server? If so are they updated? If they aren't I would get the updated versions and get rid of any 1.2.5 plugins. If the problem still occurs then delete the map and start the server again to get a new world. Tell me if this works

Yes I do have plugins. I have some questions. First how do I tell they are outdated?
Second how do I update them? Thanks for the help!!!

WOW, Thank you sooooo much it worked i deleted all my plugins cause they were outdated, and it worked. My terrain loaded perfectly!!!

Well if you haven't updated them then I think that is the problem. By update I mean the same as what you did for the craftbukkit.jar just delete them and put the 1.3.1 version of them in IF they are out. I have just seen your last response and I am going to keep this reply for future reference. Plus you're welcome!