Hail would create a random pattern; not a precision pattern as shown here.
Did you look at the roof when you purchased the house? Did you use an inspector?
I've seen and rejected roofing like this when it was delivered to a job site before installation. This is so uniform that it appears to have been stored improperly before installation.
I would find your seller and obtain, from him, the contact information for the roof replacement...assuming that it was replaced. If this is the original roof, how old is the house?
Also, you didn't answer whether the flapping that caused you to go on the roof was fixed.
Gary