Jeff, as the saying goes the devil is in the details. And Chimney flashing can be a challenge. I must admit I am having difficulty understanding what you are describing. Is there anyway you can send pictures or a sketch? In the meantime you should check your manufacturers website, they should have details showing the proper installation.
Dick Bus
2011-08-04 19:18:35.000000
I have a guy installing metal roof on a house we own. the chimney along side the house protrudes 4 inches into the roof. When he ran the panels he put a seem a few inches above the chimney on the last panel that butts up to the chimney. He said that for warranty reasons He has to cut the panel 2" above the chimney and then overlap with another panel so to allow flashing to sit on top of the lower panel and below the top panel. Is this correct? It just doesnt look good with the seem but I can accept it if it is there for a purpose.