Thanks for all the advice. I've already opened a ticket with Harmony Support via the web.

In response to gonk and PodBoy, the "Watch DVD" activity already contains a step to select the 990 DVD input. It works fine when the A/V system is already on but set to a different activity, say "Listen to CD."

The Harmony remotes keep track of whether each device is powered on. If a device needed for an activity is off, then the Activity tries to turn it on. This (I think) is where something is going wrong, since the "Watch DVD" activity works fine when the A/V system is already on.

Good suggestion on checking remotecentral.com. I'm going to head over there now!