In a recent game, my +0 Chansey's Ice Beam did 90% to a +0 Rhydon. I don't know if this is a known bug, if I'm wrong, or if I actually found something, but on the damage calculator it says that it should only deal 54.2 - 63.9%. I checked with my opponent and his DVs were all maxed, etc. Very weird.
The same guy's Rhydon was reportedly OHKOd by a Chansey BubbleBeam on ladder, which should deal 88% at the most.
Anecdotally, I've noticed that many moves which rely on the Special stat are dealing more damage than they should.
Yea, this has been an issue for a while. Please, whoever fixes this, post in here when it is fixed because I don't want to play RBY on the ladder right now since that bug is kinda huge.