Not really noticed this on the NSR yet (nmot had it long), but on my 3XV (V twin TZR - same motor layout as the NSR) the lower cylinder always smokes more - especially when it's been stood for a bit. I reason it's prob caused by the motor layout - the lower cylinder pointing down would mean that any oil in the crank cases will run down into the combustion chamber rather than sitting at the crank web end as it will on the upper cylinder. When it's standing I reckon you're bound to get a few additional dribbles from the oil feeds as well as any left in the crankcases from the last run. That's a fair amount of oil that gravity will encourage to run down and nest in the combustion chamber to freak you out the next time you start it up.
That's my theory in any case . The Aprilia is the same too FWIW.