Well, I race WERA and WSMC and have never seen a 1098R win anything BUT the twins classes. I really don't know if the issues are related to stability (my guess) or just lack of power. Don't forget, 1098R's from the factory, have the same problems all Ducati's have; poor cam timing, poor fuel mapping etc... You can't use a Nemesis on a 1098R without loosing traction control, so all of a sudden the really good tuning option, doesn't exist.
Needless to say, off the show room floor, the big twins arn't competitive against inline 4 1000's. Even Higbee on the buell from AMA, isn't able to keep up with the inline 4 1000's and he's an AMA Pro racer on a factory racing buell.
Things might change this season though, as the guys with 1098R's are dumping major coin into them. RS cam's, pistons, crank and maybe even a Mangeti Marelli ECU upgrade, might be what the doctor ordered...