I would lean heavily toward Beaker's thought and get up there on a ladder and do a test clean up on a spot, from the ladder that is and not even bother getting on the roof..
An irregularity along the seam may cause moisture to linger there and collect dirt or dust or whatever, who knows maybe it is mold.
I bet it is not a manufacture defect.
Let us know.
Also i would definitely pull the shroud down on the air conditioner in the ceiling and see if the AC is blowing cold air into the area between the ceiling and the roof and not all going into the ducting. My fifth was cooling the roof more than the inside until I got the ducking sealed up.