>>Just varying either the x or y axis gives hugely different heading results (including at 'steep' angles Nan)
>>
>
>
>

>  // Calculate compass heading
>    var compassHeading = Math.atan(Vx / Vy);
>

>
>Have you tried replacing the Math.atan()) by the Math.atan2() ?
>
>http://www.w3schools.com/jsref/jsref_atan2.asp

Hmm. Returns NaN (haven't dug into where that happens exactly)
Odd thing is it only runs once but no errors in the console.....