It's always worth checking the cheap things listed above first but this does seem to be a known problem with the EFI on the F650.
Fuel Injection FAQ
It seems that the idle is not user adjustable. If you're lucky, you'll just have to clean something. If you're unlucky, you might need to reset the EFI, replace a sensor or the EFI unit itself.
Of course, I know very little about bike mechanics in general and less about F650s. Is there an F650 forum anywhere? I post regularly in The Tenere Forum whenever my bike goes wrong and the folks there not only know the bike inside out but also happily tolerate idiots (i.e. me).
Best of luck and let us know how you get on.
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