Yeah - I just don't know how to find out what's hiding out there.
If nobody else has any other ideas, what about doing a CTRL A to select everything, then set the range of selected data to be from the beginning of the project through where you want the end to be, do a Copy Special, then build yourself a new project and paste it all in.
Pain in the rear, but at least I would think that would get you past whatever is going on in your current project.
I just don't see a lot of options, other than what had been posted, and I have not had to deal with this particular issue, so I am winging it with my suggestion above.
Now, PRIOR to doing the above, have a look at the thread in the following link, as there may be something there that helps you without having to resort to trying my above suggestion. Here is the thread link:
http://forum.cakewalk.com/Rogue-Envelope-extends-past-end-of-song-m383273.aspx Bob Bone