I have a number of other local plug-ins installed which seem not to work with the Flavour plug-in. I'm not sure if this is because of an error in our plug-ins or in the Flavour plug-in.

What happens is I get a number of mkdir warnings that the directory already exists. Then I get an error screen error/xml_writer_end_tag_no_match
line 196 of /backup/util/xml/xml_writer.class.php: xml_writer_exception thrown
line 129 of /local/flavours/flavours_packaging.class.php: call to xml_writer->end_tag()
line 63 of /local/flavours/index.php: call to flavours_packaging->packaging_execute()

If I exclude these specific plug-ins from the package, then it completes sucessfully.

One of the plug-ins I have which causes this problem is the OU's ForumNG - you can download that and try it yourself from here https://github.com/moodleou/moodle-mod_forumng. I think it probably has more complex configuration than you've previously catered for?