I hope you're waiting until the bike is warmed properly before trying to rev the engine. They don't like to rev at standstill until the water temp is hot, what you describe is similar to how a cold nc30 engine behaves when revved.
If you are warming it up properly and still seeing these symptoms, it's usually related to induction changes causing a lean midrange - removal of the rubber flap, modification of the airbox snorkel, cutting the front of the airbox base, aftermarket air filter etc. Check to see that you have part #13 in the link below:
http://www.cmsnl.com/honda-vfr400r3-199 ... _3000.html
Is it a standard Honda brand air filter that you're using?
If this is all standard then taker a look at the carb needles - there should be one 0.5mm washer under each needle as standard. An extra washer will richen up the midrange and can alleviate these sorts of symptoms, but really you'd be covering up the cause of the problem rather than fixing it.
As Jim says, how it runs can be very different when stationary it or riding it. Personally I wouldn't touch it until it's been ridden, you might just be creating more work for yourself.
