You have to use .setValueAtTime(), with the time of the marker you want to change and a MarkerValue object to change it to. Try something like this:
app.project.item(50).layer(3).property("Marker").setValueAtTime(app.project.item(50).layer(3).property("Marker").keyTime(1), new MarkerValue("New comment!"));
Walter Soyka
Designer & Mad Scientist at Keen Live [link]
Motion Graphics, Widescreen Events, Presentation Design, and Consulting
@keenlive | RenderBreak [blog] | Profile [LinkedIn]