This type of staining (algae as the other posters have said) will usually only happen on the North facing surface of the roof.  Same with condensation on your car glass.  Suprisingly, the North facing sky will actually remove heat from a substrate and thus make the roof surface colder.

Colder roof surface = condensing surface.  The moisture combined with the organic component will combine for a great growing surface (that the the rock dust organic component of the shingle).

It is not surprising that it is happeing more after you insulated the home.  By insulating (a good thing), you have reduced the heat sink between the roof and the conditioned space below and therfore made the roof colder in the process.  Colder roof...same as stated above. 

Plenty of roof washes out there that will handled most of this stuff and it does not mean the roof is cooked. 

File complaint wth the Registar of Contractors in your area. Even if they are not Lsc they should be and can face a fine.

We've done this application numerous times in southeastern PA with one subtle change, we use closed cell foam insulation directly against the underside of the roof sheathing. Open cell will continue to let air/humidity through, closed cell will not. Since air can't move through the closed cell foam there isn't any need for air flow under the roof sheathing because there won't be any humidity there to potentially condensate. Air already moves through the fiberglass insulation and that won't change when the Attic becomes conditioned space. I believe it would be best to remove ALL of the existing fiberglass ceiling insulation so that the Attic space becomes 'one' with the rest of the House. Fresh air intake to the fossil fuel furnace is necessary. It should be set up with a power damper that opens when the furnace turns on to allow combustion air directly to the heat chamber. When the furnace isn't running the damper is closed to keep unconditioned air out of the Attic.

Dennis D. Gehman, CR, MSA, CLC, CKBR, GAC, CAPS

President

Gehman Design Remodeling

NARI = National Association of the Remodeling Industry

CR = NARI Certified Remodeler

MSA = CertainTeed Master Shingle Applicator

CLC = NARI Certifled Lead Carpenter

CKBR = NARI Certified Kitchen & Bath Remodeler

GAC = Green Advantage Certified

CAPS = Certified Aging in Place Specialist

Probably need to have the skylight reflashed.  Skylights need to have special flashing kits designed for skylights.  Have a professional come to inspect to see if you have a curb mount or deck mount skylight and they will be able to give you a price to replace your current flashing with a new airtight skylight flashing kit.

Over a period of time, shingles may develop dark brown or black streaks that are sometimes mistaken for soot, dirt, moss or tree droppings.  In actuality, this discoloration may be caused by algae growth. Although most
roofing systems are susceptible to algae discoloration, it is most readily visible on white or light-colored shingles.
Today many  of the newer asphalt shingles have an Algae Resistant granular system that guards against roof algae. The system uses copper roofing granules from 3M to prevent algae growth‚ protecting the roof and preserving the home’s be auty.  Here is a link to a good explanation....  http://roofpedia.com/algae-resistant-roof-shingles/ 

Hello Terry,

What kind of roof do you have? Is it an asphalt roof? The average lifespan of asphalt composite roofs is 10-15 years. Depending on how extreme the weather is in your area, some roofs made with temporary roofing materials may start to fail as soon as eight years.  

The most common cause of this type of dark spots is a variety of blue/green algae called a  Gloeocapsa Magna. Ths stains often evolve to a moss buildup, as the algae increases moisture. That is not only an appearance problem, as algae proliferation may shorten your roof life and increase energy costs. (You mentioned you recently added more insulation to your attic. Not only that was probably not the cause, but potentially, even the need for the extra insulation is already a sign of an underperforming roof.) 

There are products on the market to clean it, but keep in mind the algae also reduces the composite integrity, so removing it may still keep your roof exposed.

It would be advised to call a professional inspector to do a roof and attic inspection. It can identify any other related issues and give you a timeframe of how much longer can your roof can hold. 

Also refer to your warranty, keeping in mind each manufacturer have a different levels of protection. 

When it's time to re-roof, you may want to consider other lifelong roofing materials (such as metal).  

Feel free to contact us if you have any other question.

Regards,

Carlos (social@interlockroofing.com)

Ventalation is one of the most important parts of your roofing system.  Has proper intake air flow coming in from the eaves of your home, where your gutters are located, and exausting through the ridge of your home.  All roofing manufactors require this as part of there warranty information because it does not only affect the condisation in your attic space but will also weaken your shingles and lower there live span.  If your home already has proper insolation and proper ventatation another option would be to add a power fan unit on your roof near the ridge with a humidistat built it.  This will turn on automatically at whatever tempature you set and also when moisture builds but will turn on.  Moisture in the attic space is common in winter months due to cold tempatures outside and heat from your attic space meeting.  I would have a roofing company come out and inspect your soffits to make sure they are ventalated and also to ensure you have a ridge vent installed on your home to start.