An upstream bug has been filed for htis issue: https://bugs.eclipse.org/bugs/show_bug.cgi?id=431973

The server runtime combo inside the server editor does not file changes to its widgets through a command manager. The server cannot realize it is dirty, and changes cannot be persisted.

A workaround is to change your runtime via the combo, and then change any other widget on the page (such as host) by adding and removing a character. The server will then know it is dirty, and saves to it will also persist your change in the runtime combo.

Until the upstream issue is fixed, this issue should remain open.