Lightmapping window opens new unity?!

I am using Unity 3.1 and when i open the lightmapping window and choose my terrain and bake it tries to open another unity program which fails to run giving the error:

Project cannot run there are 2 instances of unity opening the same project!

And when i go back to the unity window nothing responds except for the exit("X") button on the top. When i press it it gives me the option:

"continue baking" or "Exit"

I wait 20+ minutes but it does nothing and I have a small terrain.