I'm not up on the nuts and bolts of OSX apps and how the OS talks to them but in case nobody more knowledgeable answers, my guess would be this:
The OS is able to poll applications and see if they'll respond to user input; obviously this needs to happen to select something from a menu or click on a button. I assume that Activity Monitor uses something like this method to "ask" the application if it's willing to accept user input, and therefore is running normally. If the Application doesn't respond, Activity Monitor assumes that it's not responding normally, hence the message.
When the program is initially loading, it can't accept any user input, so it registers as not responding. As far as Activity Monitor can see, there's no difference between an app that you just double clicked, and one that's been running for an hour--it just knows that the process has started.
Interestingly, iDVD4 also registers as "not responding" while it's rendering DVD content, despite the fact that it is functioning normally. Just a matter of how the routines are programmed, I guess.
