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Problem is that there are installations of two different shingle manufacturing runs (since garage was built at a different time). That would be a strange coincidence. I'm curious to read more about this one. Seems you would have some collateral hail damage if it was hard enough to cause this roof damage.

Pea sized hail in the area at the largest

Right, and that would not be large enough to do damage.
Read this article: http://www.doi.ne.gov/brochure/b_hail.htm
Of course there are other sources as well, but this one really cuts to the chase

Generally, hail must be 1 ¼ inches in diameter (Half-Dollar size) before it causes damage to heavy composite shingles or wood shake shingles. Lightweight composite shingles may show damage after being struck by 1-inch diameter (Quarter size) hail. Only deteriorated composite shingles will show hail damage due to hail less than 1 inch in diameter, and the hail generally must be more than ¾ inch in diameter (Dime size).
If your area has received hail large enough to possibly cause damage to your roof, you may want to examine other objects at ground level before calling your insurance company or pulling out your ladder. Hail strong enough to damage a roof will also cause damage to nearby cars, wood fences, shutters and/or exterior siding.

Those "pock marks" do not look like hail dmg to me. If something with enough weight-inertia to damage asphalt shingles hit that roof, there would be something larger than the itsy-bitsy manifestation we see.  Usually real hail will cause some degree of a "soft spot" at the point of impact - this issue did not seem to extend below the surface of granules.

I'm not saying there has to be a visible fracture to the mat, but it often will at least have that tell-tale softness when pressed against.

What weather has this roof been subjected to for 5 years?  Hot-Lanta?

Posted By jdacree on 12 Nov 2009 07:05 PM 
... it would make the granuals on the shingles pop off like popcorn.

Not familiar with the product you refer to - but a very common one is POOR VENTILATION which will fry a roof before its time.

The damage is caused due to a saturated mat during the manufacturing of the shingle.   There was to much moisture between the fiberglass base mat and the asphalt mat when there were adhered together.    When this happens, the shingle blisters when in direct sunlight and hotter temps to allow for the moisture to exit.

Well, if there is no accidental direct physical damage resulting from the claimed Date of Loss...
It's not our duty to ID what is going on with his shingles, but I bet those manifestations were there before whatever storm occurred recently.

This shingle looks more like 10-12 then 5 years. Its 2nds or regects at best. Heat has a lot to do with this broken blisters, which could be hits by pea size.

Blisters and not covered.  Blisters are common but to this degree it is due to a out of spec run by the manufacturer.  The give away for blisters are the sharp edges seen at the pock marks.

Can't specifically tell from the photos...but do these shingles have any organic material??  What about the bird population?  I had a couple of perplexing losses a number of years ago, and we found out that pigeons, blackbirds, etc.,  found part of the shingle granules to be quite tasty.  As a previous poster mentioned, what kind of roof do the neighbors have and do they have similar signs of damage? 

I was on a roof today, only the rear slope looked like the roof in your photo.  I went into the attic and the insulation was all the way up against the soffit area, but only on the back slope.  This damage is from excessive heat build up.  My two cents for what thats worth.

Seems as though you found the answer.   I'd also consider whether the slopes are facing north-south? I wonder about the slope direction since solar exposure is an important issue in Colorado as far as direct damage from the sun. The sun is much more intense at 5,000 feet than at sea level, and CO gets over 300 sunny days a year. These 2 factors cause uneven deterioration of shingles. Shingles on the southern side become brittle / deteriorate much faster than on the north side because of excessive exposure to the sun. East and west facing slopes deteriorate more evenly than north-south slopes. If you add this to the fact that these may be low grade shingles, you may have your answer. The other issue I'd consider is the direction of the storm. As I understand it, most of the hail damage in CO was from the north (ranging from the northeast to northwest), and if the damage is on south side slopes w/ little damage to the north, then you can probably rule out hail again.

One other note about birds... I was on a commercial roof about 2-3 weeks ago, and birds had found the EPDM roof to be fun to poke into.  The landlord had contracted with an exterminator firm to get rid of the birds after having several roof leaks because of the bird damage.   When I was inspecting the covered loading docks, I found large piles of bird droppings, and there were still about 10 birds that called the building home.  I don't know what the attraction was for the birds, but this was a Class A, 45,000 square foot building, so it was not an issue of neglect on the landlord's part.   Finally, I understand that EFIS is very attractive to woodpeckers who like to live inside the EFIS layer after they knock holes into the building.