knocking sound on uphills / check engine light flashes

My 2001 Nissan Pathfinder has been making a knocking noise upon acceleration, especially on hills...and then the service engine soon light will flash for awhile, then go out. I have taken my car car into the dealership for its 60,000 mile tune up and it still does this. The car doesnt drive any differently or feel like something is wrong, its just not a good noise. I thought it might be bad gas and have changed to using better gasoline, but it still makes this noise/service engine light. Anyone else experiencing this or know what is going on?