Well.....this is not knocking problem (as far as I know) but low pickup in 2nd gear.....particularly when you go down from 3rd - 4th gear to 2nd and then try to increase speed again....
This problem was there in all units manufactured till end of August 2009 (i may be off by a couple of weeks). However, Honda Atlas managed to make appropriate changes to overcome the problem....in 4th QTR of 2009.
I recommend that you contact Honda Atlas Customer Service department and have an appointment with their engineers who use to visit each dealership once a month....and whenever any engineer visits dealership near you...take your car for an upgrade....it will take not more than 10minutes....
I did just that....early this year....and have been satisfied with the results...