2009 Subaru Forester Used Motor

I bought a 2009 forester from a dealer, and one month after the engine blew. The dealer shared the expense with me and put a used motor in the car. He told me that it was running rough but after the "drive cycles" are complete that it would clear itself up. I've been driving and operating with cars for a while now, and I've never heard of such. Here's what's happening, when you cold start it and drive it everything seems to running real smooth and good. After about 30 miles the motor begins to get loud and real rough sounding. There is no vibration in the steering wheel, and the transmission is shifting and operating smooth, but the engine sounds like a tank and you can feel it in your foot on the pedals just not right. What does this mean?