check coils. if it happens at idle, wait for bike to cool then startup and spray header pipes w/ water n see which one isnt firing. if you need to confirm problem can switch the coil to another plug and retest.
or if you have a super accurate ohmmeter can just test the coils. see this thread:
http://www.r6-forum.com/forums/showthread.php?t=233938&page=2
or if you have a super accurate ohmmeter can just test the coils. see this thread:
http://www.r6-forum.com/forums/showthread.php?t=233938&page=2