I read your answer to a question about a metal roof from April 4, 2010. I have a metal roof that I believe is leaking at the valley. The metal roof was installed over an existing shingle roof. I had the roofers also install a roof over my back deck. The back deck of course had no decking or shingle roof above it, so the roofers just framed it and covered it with metal. They installed vinyl for the ceiling. When it rains water is running down the shingles under the metal and onto the vinyl ceiling above the deck. I have removed part of the vinyl ceiling to try and locate the source of the leak. There is very little room to see since the pitch over the deck is very low. I can only tell that the water is coming in the direction of the valley.
I have caulked the screw heads and the seams where the metal laps in the direction of the roof leak, but this still has not corrected the problem. I saw in your answer to the question back in 2010 that one might consider caulking where the metal meets the valley. I am thinking about trying this as well. I assume that I should caulk both sides of the valley where the metal meets? Do you have any other suggestions?
The metal valley should be at least 24 inches wide. A sealant bead or metal building tape (ie: 440 tape from Tremco)should have been placed between the metal valley junction and the metal roof. Applying sealant to fill the gap between the valley and the metal roof may be your only alternative to stop the leak.
You could water test the valley with a hose and that would assist in pinpointing the entry location.
Best of luck.