[Porsche-O-Phile]

Residential construction is bottom-of-the-barrel in general. You'd be shocked at how often stuff like this comes up. Cheap developers, cheap/unethical builders, etc. Don't even get me started on the sales schlubs...

Anyway from the sound of it I'd be very, very surprised if there's no rot. Just because you can't see it doesn't mean it's not there. That said, there are other ways to protect under the shingles and at the valleys/changes in pitch on the roof. It sounds like a more detailed analysis is necessary but just because you don't see sheet metal doesn't necessarily mean it's detailed or built poorly (however, hearing about all the other problems doesn't exactly inspire confidence).

This sounds like a re-roof job to me. I know you don't want to tell her that, but you can only keep slapping duct-tape and chewing-gum solutions on the problem for so long...