First thing you need to do is stop trying them at stop lights and stop signs. This is a horrible idea. Why? Because this is where everyone comes to a stop. Meaning this is where everyone leaves their hunk of shit car to drip fluids everywhere while waiting for their turn to go nowhere. the first time you actually manage to do a stoppie you're going to have the front skidding out from under you and you'll go sliding into oncomming traffic. Somethin tells me your wife will like that a bit less than expensive tires.
So to answer your question
1) as Vash said, double check your clutch technique. Maybe tighten your cables up and check for play.
2) Unless you're getting seriously high, your tipover sensor shouldn't be a problem. But who knows, it might. If it is, let me know and I'll tell you how to disable it.
3) Try them with a full tank of gas. It might be something as simple and all your fuel sloshing to one side and the bike sputtering out. The simplest explaination is usually the most overlooked.
4) if you try all of these things and the bike is still sputtering, toss us some more info and we might be able to help you out. Does it only do it when the wheel comes up? Try just slowing down really fast and see if the bike dies. If you can't figure it out, then take it to a shop I guess. I'm not a fan of paying rediculous amounts to have a bike fixed and they usually don't find the prblem anyway.
5) I did a big ass writeup on stoppies and whatnot. And I'm sure there's been a few before mine. Try searching around the stunting forum and you'll find a much more detailed description on what/how to do stoppies. Good luck and be safe!
~ the super