I have an scope time out of 10 seconds set in an orchestration. This has been running for many months without any problems but today it started to timeout as soon as the messages went into the orchestration. We noticed that the time logged in HAT was about five minutes greater than the system time on the BizTalk server. We tracked this down to the SQL server being five minutes ahead of the BizTalk server.
So I changed the timeout one minutes and the timeout still occurs immediately and does not wait! Secondly we changed the timeout to ten minutes and the message processes in less than 2 seconds. Finally I synchronized two server times and reset the scope time out back to ten seconds and the messages process as they had always done.
The moral of this story is to make sure that the times of your BizTalk server and SQL server are synchronized.