Hi Chris.
With opposed piston calipers it's almost impossible to have the pistons move at exactly the same time, one piston invariably 'leads'.
On the V1000, the caliper 'floats' with the parallelogram mount having a sintered bronze bush as one of the axle spacers... This bush wears, leading to axial movement as well as radial movement and allows the caliper to float from side to side too.
So... By all means examine and rebuild the caliper - it's clearly gotten very hot. When you do, be sure to check that the fluid is returning freely from both sides as the pistons are pushed back in.
But I would definitely recommend checking the floating mount and the bush, and also the condition and adjustment of the torque arm between the rear of the crankcase and the floating caliper mount. All of the fittings should be free to move and adjusted such that the caliper is permitted to rotate freely about the axle as the suspension moves.
Hope that helps.