As ford9c stated, if you do not have a Motorcraft filter on the truck try that first. It has been stated on this forum that the cause of the "knocking" upon startup in these new engines sometimes can be attributed to oil filters with incorrect or defective antidrainback valves.

I had my cam phase sensors changed under warranty. The "knocking " noise is usually only heard after the oil has warmed up... see if you meet the criteria in the TSB 06-4-7. If you do a search on this forum, you should be able to find a post or two containing the TSB. Hopefully, someone will see this and post the TSB.