Harmony One and LG 6200 Problem

When switching activities, for example, Cable(hdmi 1) to Apple TV (hdmi 2) everything turns on respectively except input does not change. I have all the commands set up properly, therefore extremely confused. Also the tv menu comes up and blinks a couple times when switching activities. seems like something isnt configured properly but i cant figure it out. Maybe the wand?Any advice on next steps?
Edited by LGTWHIT - 1/10/13 at 3:06pm

Well, figured it out. Just bought a Yamaha 473 networking receiver with HDMI. My old receiver was only component so now I will be able to switch right through receiver instead of TV for inputs.