Brent, I am using the Harmony 676 with my 990 and experienced problems similar to yours (I'm assuming the 880 programming is similar). I had to go into the 'adjust power settings' for the 990 and change the power on command to 'InputVideo1'. I also had to change the power on delay to about 4 seconds otherwise the 990 would not receive the input select command that follows the power on command. I tried setting the power on command to a blank command knowing that the following input select command would power on the 990 (trying to avoid that 4 second delay) but this did not work. I assume the Harmony loses it's stateful information if there is not a power on or power toggle type command assigned.

Keep us posted on what you find, there has got to be a better way to handle the power on for the 990.