Hi Paul,
Thanks for that. It's just the link I gave earlier, namely
Rankwell Blog Archive Htaccess for addon domains and several other forums seem to suggest there is a danger of being penalised because it appears to the search engines that your have two sites with duplicated content when the spiders crawl them - namely addondomain.com and addondomain.maindomain.com, even though it's actually only one site.
Thanks
Wes