Can you tell if the knock is in the top part of the motor or the bottom ? If it is in the top, you could have a lobe on the camshaft or lifter that is wiped out. The first 30 minutes of running a new engine is the most critical time. This happens every now and then when breaking in a new engine. Normally it is recommended that you use a special additive or a special motor oil that is high in zinc during the break in process to eliminate this problem. Did they send you any special instructions for breaking the engine in ?
If the knock is in the bottom of the motor it very likely is a rod bearing or possibly a main bearing. This type of issue will only get worse and if left unattended will most certainly result in major engine failure. One of the first things I would do is drain the oil and get a strainer (paint strainer will work) and strain the oil and see if you notice any bright silver or copper particles in the oil and filter. If you notice these particles you can be pretty sure that you have wiped out a main or rod bearing. You will also normally notice a gradual loss in oil pressure as the clearances between the crank and bearings begin to steadily get larger.
Regardless of the problem; I would definitely demand that they send me another engine. No one should have to go through such a run around such as this after making a new purchase that is under warranty.
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