I had the same problem as you can read in this thread here
http://www.xt660.com/showthread.php?t=26643
I cleaned the bobbins, no difference.
I checked the caliper sliders - all nice and greased and not sticking.
I checked the wheel bearings - all ok.
I ended up buying some new discs and fitted them at the weekend. Bike feels so much better now.
I bought a pair of new oem front discs from Fowlers parts as they were only �95 for the pair including postage. Local Yamaha dealer was quoting �87 each!