Assuming Stop At Project End is still enabled, I'm guessing there's an automation node or something further out in the timeline defining the end. Hit Ctrl+End to find the stopping point if you haven't already, and check for data of any kind. Or you can just set the Now time at the musical end and use keyboard shortcuts to set From = Now, and Thru = End ( I don't recall the new default keyboard shortcuts), select all tracks and delete everything in that range.