OK so this was to do with a launcher that I was using, and in the launcher I had the option to relaunch the course if it had not worked correctly. If you did this when the course had already launched itself (but you didn't notice it in a new tab, and launched the course again with my link (which users were doing), then it tracked the first launch of the window not the new one).

A quick rewrite of the launcher page and *hopefully* that has fixed it.