What I believe happens is Yamaha check the bikes as the leave the factory and set the roughly set the idle, roughly being all you can do on a brand new "tight" engine. They then arrive at the dealers, who assemble the bike and should check it again prior to delivery, but again with a tight motor and after a usually very short ride (not ideal). As the engine loosens the idle settles and more often than not the dealer doesn't check and adjust idle properly at services thereafter - don't get the engine warm enough, don't ride it far enough, maybe they can't be bothered to enter diag screen, or probably they just simply check that it idles on the stand with out stalling.

Anyhow here's a thread which explains how to get the rev counter up on the dash and how to adjust the idle...

http://www.xt660.com/showthread.php?t=801

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