Hey Kevin, thanks for the reply mate!
Taking on your advice, I replaced the Pixhawk power module with a new one and went about the same test.
…unfortunately this resulted in the same situation 
Reading this post here about max current and thrusters, I am maybe starting to think that by expanding my battery capacity to 3600mAh, the thrusters now have far more current than in a standard BlueRov setup to draw from - in turn allowing for more than the 30-60A recommend continuous current draw that the Pixhawk power module is rated for. Was thinking about using a High current meter like this one here to do the same job.
Would love to know your thoughts on this!
Cheers,
Jordan