Hey guys mine was EXACTLY the same from new and I notified the dealer as I thought that we would need a gearbox strip. Mine was a noisy 4th gear. Anyway after about 5000 km the noise went away and Martin told me that often they need to be run in and that so far they have NEVER had to strip a gear box on a 660, neither MT03 nor XTs.

So dont worry you should be ok!!!

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(Now sold on, sob) 2011 Blue XT660X with gold wheels, was 26,500 km.
Engine mods: K&N Stage 1 filter, DNA Stage 2 filter, snorkel removed, Kev fuel mod fitted.
Plus: smoked Puig screen, Yam aluminium sump guard, Yamaha / Acerbis handguards, Givi Trekker aluminium side cases, Leo Vince X3 cans plus Kev front fork mod and Fender Xtender. Just fitted Michelin Road Pilot 3 tyres.

SOLD the XTX for a Super Ten 1200. And just bought a Raptor 700 so staying on here for some tips....