The R6 is known for having a really notchy, quick-engaging transmission. I've been riding my '05 for almost a year now and I still have crappy shifts sometimes. Any time you shift quickly and release the clutch quickly when you're up at high rpm, the forks will unload a bit. You're probably not revving high enough to make it hop in third, but it will do that in third, 4th and 5th if you're way up in the power band
To make things smoother, try revving to around 8k in between shifts. On my '05, that seems to be a good transition point. Don't let the rpm drop too far while you're shifting, try to hold the engine around 7-8k, and then release the clutch. Don't just let it pop back out, that's what makes the bike hop. Release it smoothly taking about half a second to release it. It takes time to get used to, but it will really help make the bike smoother.