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I have just bought some new Shimano PD-R540 SPD-SL (look style, not 2 bolt) pedals and there is an extremely annoying clicking noise that seems to be coming from the right side only, I have put a little bit of dry lube on the cleats but that didn't fix it. Any suggestion?
 

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la dolce vita
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Tension may be too low on that pedal. Try cranking it up a notch and see if it goes away.
 

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It isn't always coming from where you think it's coming from....

You many find the following links helpful in tracking it down:

http://sheldonbrown.com/creaks.html

AND

http://www.parktool.com/repair/readhowto.asp?id=123

It's usually just a matter of patiently removing, cleaning,
re-lubing, and re-torquing fasteners until it quiets down.

Can also be shoelace 'aglet' hitting crank arm, FD cable end crimp hitting crank arm, etc., etc., etc.
 

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I had similar problem on MTB version of the pedal. I called Shimano, they said to remove the pedal axle assembly out of the pedal body, then fill it up with waterproof grease and retighten the pedal axle assembly inonto pedal body, wipe off the excess grease that comes out or squezes out. I did not have problem for 4 years after that. I just repeated the procedure and hope to do another 4 years on those pedals.
When removing the pedal axle assembly(1) from the pedal body please not the direction on the lock bolt (2) for loosening/tightening it is different on right and left pedal
here are the tech docs
http://techdocs.shimano.com/media/t...PD/EV-PD-R540-2304A_v1_m56577569830608623.pdf
 

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Orbea-Ultegra-MavicCosmicPro
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I have just bought some new Shimano PD-R540 SPD-SL (look style, not 2 bolt) pedals and there is an extremely annoying clicking noise that seems to be coming from the right side only, I have put a little bit of dry lube on the cleats but that didn't fix it. Any suggestion?
Annoying CLICKING shimano pedals. Because the pedal thread and cranks are different materials and perhaps even slightly different in thread, they sometimes click. To stop this use plumbers teflon tape wrap at least 7 times around the pedal thread and screw back into crank to a snug fit. Noise gone problem solved.
 

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Banned Sock Puppet
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Annoying CLICKING shimano pedals. Because the pedal thread and cranks are different materials and perhaps even slightly different in thread, they sometimes click. To stop this use plumbers teflon tape wrap at least 7 times around the pedal thread and screw back into crank to a snug fit. Noise gone problem solved.
Some grease on the threads works just as well.
 
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