Looks as if I didn't inspect the link closely enough the first time. The broken links look like this:
The requested URL /file.php/8/Lesson12_files/Lesson12.htm was not found on this server.
This happens on labels and links to internal uploaded pages.
I used this fix and it worked:
http://moodle.org/mod/forum/discuss.php?d=19804&parent=93904
Thanks Martin