Mikepier wrote:
Here are the pics. Where you see my red caulking gun is where the roof
leak is in the attic. As you can see this is a split level house, and
although there is an adjacent wall joining the roof, I do not think it
is coming from there because there is a soffit overhang as you can see
and it's pretty dry underneath there and usually does not get that wet
in the rain.
http://mp656.photosite.com/roofleak/

The stain is from that area taking longer to dry out than the rest of
the roof. You said that water was coming out from underneath the
shingles when you lifted them - that water would drain down slowly and
keep the shingle surface moist allowing stuff to grow (stain).

From the looks of it, I'd guess that the water is getting under the
shingles where that valley terminates near the end of the gutter. If
they didn't flash that area correctly, you won't be able to fix it with
dabs of roofing cement. That'll only get in your way later when you
have to remove nails/shingles.

It's entirely possible that the shingles/flashing look fine from the
surface, but that there's something wrong underneath. The first thing
I'd do would be to start looking more closely at that valley
termination. You may have to remove the section of gutter over the
roof and pull a few shingles. Pulling shingles in colder weather is a
pain in the ass as they're not very flexible and you can crack a
shingle pretty easily.

Post some pictures of that valley termination with greater detail - the
pictures you posted are pretty small.

R