So we focus on customization only really here, but I appreciate there are not many forums yet. If issues remains I recommend Oracle Support's communities who have install/upgrade experts.
I found this similar post that also gives a test and something else to look for (a downgrade statement in the log). Both are worth checking for.
Above also mentions to check the SOA Servers, which whilst might be a red herring all output is worth considering.
FA Dev Relations: blogs.oracle.com/fadevrel