Shimano offers the shifter as a separate unit in the XT and XTR systems. This allows you to upgrade to the V-brake lever of your choice while keeping the RapidFire shifting system from Shimano. After the first ride I was hearing clicking noises coming from the crank area. I had only put 10-15 miles on this bike before it made these noises. A loose crank-arm fixing bolt could cause some noise, though typically that is a creaking sound, not a clicking.
Clicks tend to come form other areas.
Basically, with any noise you have to use the process of elimination. If the answer is yes to the last two, it's probably something as simple as the front derailleur cable hitting the crank. If it clicks only when you're in the big ring, the front derailleur cage might be hitting the crank arm. Like we said, you'll have to use the process of elimination to find out.