Well, after troubleshooting with tier-two support, power-on delays weren't the answer. Sending infrared delays on the startup of each activity was the answer. The key value for me was 3.5 seconds of delay.
Another note, the actual infrared commands being sent to the 990 from the 880 is a "InputVideo1" for startup immediately followed by the respective input for your activity, like "InputDVD". I have a hunch the original 990 remote is not doing this.
I asked the guy if my account could be changed to send simply "InputDVD" for startup and if their software had to, re-send "InputDVD" and he said they could, but he wanted to test the activity delays and by the time we were done, I just needed to get off the phone. So, I wonder what would've happened.
I'm curious, if someone else has the 880, I noticed a pattern which we fixed. I wonder if anyone else has the problem and just hasn't noticed it. Try turning on the 990 with the "Listen to Radio" activity. Turn it back off. Then do "Listen to Radio" again. I was having issues starting the 990 on an input that it was on before previously shutting it down. If I was on Video 1, turned it off, and then did "Listen to Radio", it would work.
I could go on with lots of more details, but I won't. It works now, with the 3.5 second activity delay. If I get the notion, maybe I'll call them back and ask them to update my profile to startup the 990 by actually sending the real input (rather that video1), just like the original 990 remote. I have a hunch that would remove all issues.