I had the same issue quite some time back. After troubleshooting a lot, Harmony customer support gave me the info that their code for starting the 990 regardless of your activity is to start it with Video1, then based on your activity they send a secondary signal. The issue for me was that the secondary signal was getting mixed up with other various signals being sent when trying to power on other components. Actually, probably the other signals being sent out were actually occupying the 990 and preventing it from seeing the secondary signal.
I really wish they would've just programed the 880 to exactly match the original 990's remote.
The only solution I found was with the power on delays and such. It took quite a bit of trial and error. I think changing the delays on my other components is what eventually got it to work for me. That way the 880 wasn't sending out various signals to other components until the 990 had a chance to get started up.
Hope that helps. I know, it's annoying. Plus, tier 1 support at Harmony was next to no help but eventually I was passed up the line to tier 2 support and they were actually very helpful.