Diggs,
Now I understand your configuration and the mis-understanding.
You previously stated that the Motorola Comcast box was controlled directly from the Beo5, based on your feedback this is NOT the case, it is controlled by the STB-C.
The reason you have the problem with the power button is almost certainly because one "toggles" the power off/on and the other has a seperate "off" and "on"signal.
I have had a look at the DCT6208HD which uses 32 bit NEC protocol and the power is a "toggle" on/off and has a HEX command code of "F9"
To fix the problem you could switch the Comcast box off/on DIRECTLY from the Beo5. To implement this option we would need to establish the "off/on" HEX codes and I expect this boxes uses the standard codes and a small XML file would need to be created and then added to your configuration.