Hi Charlie,
Open up the email and look at the HTML Do you see "mktNoTrack" anywhere? If so, open up the hyperlink editor in the WYSIWYG editor and look at the advanced options. That's where you can turn the tracking on or off.
These two articles may help too:
https://community.marketo.com/MarketoArticle?id=kA050000000KyqCCAS
https://community.marketo.com/MarketoArticle?id=kA050000000KypwCAC
Thanks,
Vivi