Facing TV Problems? Ask a TV Technician.
You need to actually tell the remote to change to the Input you want when you turn on the TV. This is done through the Harmony software. Did you program the Harmony remote, or did somebody else?
Also what's the model number off the back of the TV? I've setup dozens of Harmony remote, and the software always asks what "Input" you need to perform an activity (watch TV, watch movie, etc.).