@Turk I had a good warranty experience for my transmission, however, that's certainly based on the dealer and not Triumph themselves.
Sounds like Cliff doesn't know what the **** he's talking about. The R3 DID have a dog issue on 2nd gear early on, so they updated 2nd to have 1/2 as many dogs as originally and the problem there was fixed. The problem NOW is that the bikes are being assembled wrong, leading to poping out of gear, and each time it pops out it slightly rounds the corner of the dog and the slot on the gear. Eventually, you end up with semi-circle dogs and very rounded slots and it wont stay in gear.
My two running theories are: Slightly bent shift fork when originally installed, triumph source the forks from someone and who's to say they actually checked for straightness prior to installing. The alternate theory, the one I have for my bike, is missing shim/spacer in the assembly leading to too close a tolerance, leading to a bend fork, leading to the above problem.
They've warrantied a number of them for these issues, at least 3 just on these forums, over the last year. They know about it, they just don't give a **** because the R3 is a dying breed.