well I seem to have solved the problem for the time being. I don't think it was anything to do with the file, it was moodle's file system. I regularly wipe a number of files out, upload a zip and unzip the same updated files in much the same folders. Every so often moodle seems to have not wiped the old file because opening what should be the new file actually opens the old file. The workaround is to put the root in a slightly different place and then the 'old' file is lost and moodle finds the new file.
Is this something that is known about? Has it been sorted in 1.3? It seems very wierd.
Richard