I also ran into same problems when we upgraded from Jdev 22.214.171.124 to 126.96.36.199. In the pages where we have regions, we saw the same warnings :
2013-09-24 10:05:30,270 [ [ACTIVE] ExecuteThread: '3' for queue: 'weblogic.kernel.Default (self-tuning)' ] WARN oracle.adfinternal.controller.state.ControllerState - ADFc: No view port found with ID ......
Did you opened an SR? Can you please share how you have resolved this problem?