The 3-yr/36,000 mile warranty covers your car systems and parts with the exception of items of natural wear. It is within reason that by the 29,000 mark, the ORIGINAL brake pads would be fully worn, and even that with heavy use the brake rotors could be deformed.

HOWEVER--your case should be viewed differently if brake pads have not had 29,000 miles of use because they have been replaced more than once during that mileage. Also since there is a known issue with the braking system, they should be fixed for you again as a demonstration of good will.

It sounds like your dealer is being a real problem about this, and if I were you I would get in touch with Honda Customer Care.

Out of curiousity, I'd like to know if those of us with braking problems have a Japanese-built (VIN begins with J) or American-built. Mine is Japanese.