Firstly I have had a couple of faults which have been sorted through this forum, so thank you for all the great info.
Back to my issue, when ROV connected to QGC the horizon is 90 degrees out. When in sensors page and carryout the Level Horizon it straight away comes up with calibration failed. I have carried out accelerometer calibration and that is all good.
The electronics enclosure is positioned in the tube with the Pixhawk on the starboard side as per the assembly drawings show.
I have carried out a level horizon with the Pixhawk on top, and then it works!
So is there somewhere in the software where the horizon can be offset 90 degrees? Other than ‘level horizon’ or does the Pixhawk have to be on top in the enclosure?