The dealer did not mean that the oil filter would make the noise. What he was saying was the motorcraft filters have a check valve that prevents oil from flowing back out of it when the engine is off. Without this valve it could take a couple of seconds for your truck to build oil pressure. So things like trimming chain tensioner and lifters will not have oil pressure right away. I am not sure if the filters other than motorcraft have check valves or not.
My guess would be you are hearing the starter bendix stay engaged for too long, or worse case timming chain noise either due to lack of oil pressure at start up or a guide that is damaged.
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I have the same issue as this, the engine was cold on startup, started up and you can hear a chattering sound for about 2-3 seconds and then it goes away, cant hear it again until the motor is pure cold again, never gave me any issues, brought it into the dealer and they thought it was the chain tensioner because the ford hotline told them to change that. Turns out they took it apart again and found wear on the cam caps and dropped the oil pan and found wear on some bearings (not sure) now they are putting a new motor in. Strange but Ill take that! haha
Hey guys. Got my truck back with the work order. It says gears and chain worn bad. Removed mains and rods, mains worn bad. Cam caps and cam worn. They gave me a new long block and gaskets. Hope this helps. Sounds like a major issue, btw its a 2011 fx4 ecoboost