Any one have this problem before?

I got a 1998 Ninja ZX-6R back in November. The thing runs great. I changed the spark plugs, cleaned the air filter, I had a stuck float and I changed the oil every three thousand miles. It runs better now than when I first got it cause it sat for almost a year. My problem is that in the past three months the bike will just flat out stall when I pull the clutch in. It does this either when I am up shifting, down shifting, or any gear for that matter. My Ninja just doesn't care. It fires right back up when I push the starter button and it runs flawless. Is this a common thing with the 1998 NInja or something else wrong. Obviously it ain't nothing major. It just annoys me. I would appreiate it if someone responded. I posted this on another sight and got nothing back. I ain't making this up.
One more thing I have a Yosh RS-3 slip on. It ain't jetted. When I changed the plugs the old ones were the right color.

Thanks,
Matt
Here's my ten cents. My two cents is free.