My first '07 had a similar issue which made the bike almost unrideable.
As those above I tuned it with tune ECU,
I had two 990's at the time one ran fine so I changed ECU's throttle
bodies, sensors, etc.with no luck.
Finally I got the bike back to running like it should by making fine adjustments
to the small screw which adjusts the throttle position on start up.
That's on the underside of the small electrical/mechanical sensor on the front
right side of the FI's
I removed the airbox and reinstalled the injectors and made the adjustments with the bike running.
Just a small adjustment was enough.
Hope this helps.
Martyn, I got the bike from the shipper and am now in Mazatlan after
riding a 1500 mile loop through Northern Mexico ( Copper Canyon
Durango, etc )
We are headed South and with luck hope to see you in Chile.
Da oggi la strada
é senza limiti