We've found out what the problems were, so am sharing here in case others have made teh same mistake.
Basically we've narrowed down the most likely answer to be that I had sent myself a sample, and as such none of the email tracking is included, this is expected behaviour but we missed it.
Also, and this may be obvious but might help others, the link to the template is broken if you change the html code. so for example, we built an email from a template, then changed the header image in the html code, so as a consequence the original template is no longer being used - but importantly the tracking still works. As I said, might be obvious to most but we missed it.