Mine did that alot at first - brand new 03 - my idle was too low and I was not allowing enough warm up time. Super Duper race car-like motor should be properly warmed up first before driven:
1. turn key and note initial clock time
2. wait for whiney fuel thingy to shutup and then start it
3. use fast idle for 45 seconds, then turn down to 1200 rpm
4. put on all your gear: gloves, helmet, pants, coat, check your boots, position nut cup - stall tactic for more warm up time.
5. tie down your crap, or slowly rub your hump in admiration
6. do your walk around and check tire presure, check your lights, reflectors, brake light, look for oil
7. mount the bike, stand up right, adjust yoru mirrors, kick stand up, clutch in, put in first gear so THAT can warm up
8. note the clock time and sit there ready until it turns over to the NEXT minute and then take off
I try to warm up for 3-5 minutes and haven't had that problem since.