Well, yesterday I rebuiult the project file (including entering the chapter marks by hand) using the two CC-created content files (.m2v & wav) and then hit build. It seemed to be running ok then came up with a small dialog with just 'access denied' in it. This error was quite reproducible, and using Microsoft's Process Monitor I found it wanted to create am .xmp file for the Encore Library asset I was using (the Projector one). I gave my account write access to that folder and it got further and then hit another 'access denied' : looks the same, but this time for another file in the Program Files/Common/Adobe folder...
Getting fed up with this 
Is there any other tool I can use to make a DVD from my film? Encore seems to be absolutely riddled with bugs.
Edit: the current 'access denied' is to the file "C:\Program Files (x86)\Adobe\Adobe Encore CS4\DualLayerVideoTSLayout.log"
which doesn't even exist!