EvilJack,
check the manual for EZ-Sync, Viera Link. They have renamed this so many times it gets stupid.
You have given me a clue as to what is happening here. It seems that you are not sending discrete On/Off commands to your TV.
Try testing the Discrete On/Off Commands in Device mode and see if they are actually On and Off and not just Power Toggle.
From what you both are saying, it seems that the Harmony is sending the Power Toggle command and not the On command.
If this is the case then there may be a solution by changing the way the TV powers on in the Harmony set up OR get Harmony support to put in the discrete commands for you, in your profile.
I ,myself, prefer the discrete commands.