This is a somewhat common problem. It's not your shifting. Mine has been fine(knocks on wood) and I don't "pussyfoot" it. I'm pretty sure it is a matter of getting the clearances on the spring correct during the install. Here are a couple of posts, not Hyper specific but relevant.
A post on SMJ by KTM560SMR...
FWIW We had a 1098 in today with 720 miles that had a broken spring on the articulating shift arm, same as yours. The spring broke because the shift arm was mal-adjusted from the factory. When the shift arm is out of adjustment, the spring can actually contact the timing gear on the crankshaft on downshifts, ultimately wearing through and breaking the spring. Putting a new spring without adjusting the arm correctly will not correct the problem, obviously. There is a special tool that fits on the end of the shift drum, WITH THE TRANNY PLACED IN SECOND GEAR, you align the marking-line in the arm up with the end of the tool. Then you can check your work by temporarily fitting the shift linkage with the alternator cover still off, and pressing down (simulating downshift), there should be approx 4-6mm clearance between the spring and the crank gear. That should cure the problem, as that gearbox is essentially the same gearbox they have used with great success for 20+ years now, they have been BULLETPROOF! I suppose you COULD have an internal issue, but I would be VERY SURPRISED!!!!!! Keep us informed...
And another post from KTM560SMR...
Yes, I am a tech at a dealer in New York. I was bitten by "Ducati passion" in 1991, bought my 1st in 93 (888) and have owned/serviced/raced them ever since. I actually get to fly to Bologna in two weeks for a week for training on the DesmosediciRR streetbike that is being released shortly-tough job right?
Anyways, I'm sure you have a strong dealer and the bike is in good hands, I only brought it up because it might not occur to a guy that the gear selector would contact the crank timing gear. It is the same gear selector arm they have used since FOREVER- 851/888/748/9X6/Monster/Supersport/Multi etc etc... , but the timing gear is changed and is much larger (stronger for all the extra HP these things make now) and so I think the fine adjustment on that arm is more critical than it used to be. Any tech who has adjusted more than 5 or 10 on say a 916 or whatever could do one by eye without the tool, you simply want to achieve equal travel for and aft in 2nd/3rd gear, and a mm one way or the other may not effect shift quality. But with the reduced clearance on the new models, I think we all need to dust off the special tool because the tolerance is much tighter, I suppose.And even then we need to take the extra step to check the clearance with the gear, and maybe "cheat" the other way if necessary to assure clearance with the gear????? Because keep in mind, the Motard riding style of stomping downshift late on corner entry is not the same as the finesse you might apply to a 996 pedal...Best of luck with it, I'm sure your dealer and area tech rep will get it figured out shortly, Ducati has great service personel, and you will enjoy your bike again for many 1000s of miles
__________________
And a link to a thread about the problem.
http://www.ducati.ms/forums/showthread.php?t=43425&highlight=stuck+shifter
Hope it works out for everyone involved.Keep us posted...I love my Hyper.
arty
I'll be hitting you up for some more Skaggs action in the near future. 
) then they are just replacing the broken parts with the same crap that broke the first time. The mfg is telling the dealer what to do and how to fix it......if you want to pay out of your pocket then they can install the "fix" and be done with it. This sucks....and it seems like the dealer is probably getting frustrated with these issues also, no excuse for them to make you feel like you are being pushed aside....but lots of times it is not as easy for the dealer to do what the customer wants....especially for free under warranty....the mfg is controling that fix
