Shelley works on the bug - 137822 and log all detailed information about the bug via her blog http://xiajunshi.wordpress.com/
I saw her last post yesterday and she was very close to fix the bug so I think it is time to give her a hand
Her recent investigations are very specific and accurate. It saves me a lot time to look the bug all over again and she points out the exact location where I need to start.
Here is the possible solution to the Bug - 137822 (Wait for Shelley's confirmation)
Before I go into the solution, let me describe what causes this bug.
If I have a Server in the "Servers View" tab, I need to initialize the ILaunchConfigurationWorkingCopy before I run a New_configuration, in Apache Tomcat, Run Configurations. The problem is that the ServerLaunchConfigurationTab class does not set up ILaunchConfigurationWorkingCopy wc from the void initializeFrom(ILaunchConfiguration configuration) method before calling the void handleServerSelection().
Solution of the Bug
In the public void initializeFrom(ILaunchConfiguration configuration) method, org.eclipse.wst.server.ui.ServerLaunchConfiguration Class, sets the ILaunchConfigurationWorkingCopy (Detail - See Screenshot below)
Shelley, please confirm the fix.