I had a similar problem though my panel deals with the selected layer. Sometimes the selected layer changed without any of the event handlers I set up being called. I ended up adding an 'update panel' button to the panel so the user could update the panel instead of switching back and forth between layers until an event handler was called.
In testing this bug, I noticed that if I run a script on opening a document, all documents will be cycled through when opening multiple files at once. This will work, but is not optimal.
I don't have this behavior with CS4.
Opening several docs then defining the notifier for all events, then selecting an inactive document: the script is called on a "select" event.
When the notifier is already defined, the open command of several docs raises the good number of "open" events, but only the first has some arguments (file path) and the next have not ??.