Hi Sam,
the very first step is to activate the API logging to record how the Content reacts in terms of tracking calls in the different scenarios, including to look at the manifest file to see if a Mastery Score has been set there.
If the Content doesn't talk with Moodle, via the SCORM API, enough to track the relevant data, your reports will be blank in any LMS: the key point is to identify what the Content misses to tell about the User's experience and when. Then you can start looking at the JS code of your Content to address most of the problems, the why part of the game.
You can't be sure that Network and Session issues will be 100% under your control so expect at least a 2-5% of "strange" tracking situations, if you can't control OS, Browser, Network and Bandwidth of your Users.
HTH,
Matteo