Looks like the changes made in BridgeSetup.java for ICE-4552 have broken window scope feature.
Invoking WindowScopeManager.determineWindowID method during render phase is not appropriate because the thread locals are setup to late in the process. WindowELResolver needs to thread local set as soon as restore-phase is executed.

Invoke WindowScopeManager.determineWindowID before restore phase is invoked. Refactor tests in 'renderView' method. Remove unused WindowSCopeSetup class.

New stack trace that is inconsistent but causes no problem with application...

INFO: Server startup in 11028 ms
java.lang.RuntimeException: Unknown window scope ID: 1261070254294
at org.icefaces.application.WindowScopeManager.determineWindowID(WindowScopeManager.java:64)
at org.icefaces.push.BridgeSetup.createView(BridgeSetup.java:32)
at com.sun.faces.application.view.ViewMetadataImpl.createMetadataView(ViewMetadataImpl.java:101)
at com.sun.faces.application.view.StateManagementStrategyImpl.restoreView(StateManagementStrategyImpl.java:200)
at com.sun.faces.application.StateManagerImpl.restoreView(StateManagerImpl.java:177)
at com.sun.faces.application.view.ViewHandlingStrategy.restoreView(ViewHandlingStrategy.java:131)
at com.sun.faces.application.view.FaceletViewHandlingStrategy.restoreView(FaceletViewHandlingStrategy.java:429)
at com.sun.faces.application.view.MultiViewHandler.restoreView(MultiViewHandler.java:143)
at javax.faces.application.ViewHandlerWrapper.restoreView(ViewHandlerWrapper.java:288)
at javax.faces.application.ViewHandlerWrapper.restoreView(ViewHandlerWrapper.java:288)
at com.sun.faces.lifecycle.RestoreViewPhase.execute(RestoreViewPhase.java:199)
at com.sun.faces.lifecycle.Phase.doPhase(Phase.java:101)
at com.sun.faces.lifecycle.RestoreViewPhase.doPhase(RestoreViewPhase.java:110)
at com.sun.faces.lifecycle.LifecycleImpl.execute(LifecycleImpl.java:118)
at javax.faces.webapp.FacesServlet.service(FacesServlet.java:310)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:128)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:293)
at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:849)
at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:583)
at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:454)
at java.lang.Thread.run(Thread.java:619)
java.lang.NullPointerException
at org.icefaces.event.DetectNavigationPhaseListener.afterPhase(DetectNavigationPhaseListener.java:54)
at com.sun.faces.lifecycle.Phase.handleAfterPhase(Phase.java:189)
at com.sun.faces.lifecycle.Phase.doPhase(Phase.java:107)
at com.sun.faces.lifecycle.RestoreViewPhase.doPhase(RestoreViewPhase.java:110)
at com.sun.faces.lifecycle.LifecycleImpl.execute(LifecycleImpl.java:118)
at javax.faces.webapp.FacesServlet.service(FacesServlet.java:310)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:128)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:293)
at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:849)
at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:583)
at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:454)
at java.lang.Thread.run(Thread.java:619)
Dec 17, 2009 10:21:29 AM org.apache.catalina.core.StandardWrapperValve invoke
SEVERE: Servlet.service() for servlet Faces Servlet threw exception
java.lang.NullPointerException
at java.io.Writer.write(Writer.java:140)
at com.sun.faces.context.AjaxExceptionHandlerImpl.handlePartialResponseError(AjaxExceptionHandlerImpl.java:200)
at com.sun.faces.context.AjaxExceptionHandlerImpl.handle(AjaxExceptionHandlerImpl.java:119)
at com.sun.faces.lifecycle.Phase.doPhase(Phase.java:119)
at com.sun.faces.lifecycle.RestoreViewPhase.doPhase(RestoreViewPhase.java:110)
at com.sun.faces.lifecycle.LifecycleImpl.execute(LifecycleImpl.java:118)
at javax.faces.webapp.FacesServlet.service(FacesServlet.java:310)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:128)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:293)
at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:849)
at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:583)
at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:454)
at java.lang.Thread.run(Thread.java:619)

Commit #20021 for ICE-5224 fixes the RuntimeException. 'ice.window' and 'javax.faces.ViewState' hidden fields are no longer cleared.