Do you have the latest firmware installed on your Pro unit? If you don't it has a power tracking feature that should help keep this from happening, so you should update to the latest firmware.
If you already have the latest firmware installed then I am going to guess that you are turning the PS3 off by some other means than switching activities or hitting the all off button on your remote. You can't do that if you expect the power tracking feature to be able to work correctly. You should only shut the PS3 off using the PowerOff command on your Harmony remote (or by having the Harmony remote automatically send the PowerOff command when you switch activities or hit the all off button).