This happens a lot. I try to open craftbukkit-0.0.1-SNAPSHOT and the interface doesn't open and the server isn't running. But when i go to the task manager the javaw.exe *32 is running. The only solution I found was re installing craftbukkit.
Double clicking the craftbukkit.jar file is the wrong way to launch the server. Do not do it this way - read the wiki on how to set it up.