Problem appears after importing old workspace(created before servers .org group separation).
For example - i want to change in this imported workspace server configuration. I'll go to preferences, select runtime, press Edit button. Look at screenshot. In old versions runtime was 4.2 for all types. Now it separated to JBoss EAP 4.3 and others. So if you try to edit old runtime for EAP server - you can't do this, because wizard thinks that this is simple 4.2 runtime and shows warning.
So users with old workspaces and JBoss EAP or SOAP servers will get some troubles. So warning must be changed to show user that he need to remake runtime. Or new button(back button enabled) added to add posibility to change runtime type.