About the most comfortable shoes I've ever owned - I love them !
The only problem I've had is that when they get wet, and you then run down steep hills, the insole rucks up as it is not stiff enough. I've now replaced the standard insole with a much stiffer one from a pair of Nike Pegasus.
So, for the OP, then you could always try a stiffer insole, but no idea why you are feeling the lugs, maybe the soles of your feet just need to harden up a bit ?