hahagal,
Sorry that you are seeing this issue.
Can you please give us some more information to help investigate further ?
1. Please share the Build ID from Help > About. Also share the version details of the WAS server.
2. How big is your project ?
3. Can you please try the In-Workspace deployment mode and see if it helps?
4. I suggest you give MyEclipse Blue 2013 a try. The Classic mode is faster than previous versions of Blue. You can download MEB 2013 from here :
https://www.myeclipseide.com/index.php?name=Recommend_Us&req=Download&version=MEBlue
Let us know how it works for you.