(First off, note that this is not an Eclipse support forum, and I can't help with Eclipse specific problems at all.)
Extract required libraries into generated jars
This sounds scary, what exactly does this do?
I recommend not merging contents of other libraries into your own jar. You might run into licensing troubles - not concerning JSFML, but generally this is an issue. Rather set your jar's classpath in the manifest to jsfml.jar and deploy that separately. It's also easier to update if ever necessary.
the window pops up and the rest of the window is blank white. Then it stops responding.
Is it your game's window? If so, sounds to me like resources can't be found. You share too little information about your project, though, so I cannot really help here.
Make sure that your resources are available in the deployed version. If you load them from the classpath, make sure they're in your jar file. If you load them file-based, you cannot contain them in your jar, but you need to deploy the directory as it is in your development environment.