Do a small test case. Start a new application using the new version and do a navigation with pages having regions there.If you don't get the error you can compare the files. If you still get the error you can open an SR with support and ask them to look into it.
I also ran into same problems when we upgraded from Jdev 126.96.36.199 to 188.8.131.52. 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?