I have built one of the 2.8 Controller Boards with the new HD-Pro Camera Upgrade and have checked it out functionally on my test bench wiring harness though I have not installed it in the WTC.
To the best of my knowledge the alignment of the Controller Board in the WTC is dictated by the position of the DB-25 connector mounted on the Pass-Through End Cap. Any misalignment of the DB-25 connector on the End Cap or a misalignment of the Pass-Though End Cap plates could cause the Controller Board to be misaligned in the WTC causing the O ring straps to contact the inside of the WTC?
However, I just took a look at my 2.8 Controller Board with the new HD-Pro Camera Upgrade and determined that the O ring straps should not hit the inside of the WTC if the Camera Platform has been assembled and installed correctly on the Electronics Chassis.
You can verify the correct assembly and installation of the Camera Platform in the Electronics Chassis by laying the Electronics Chassis with the camera facing down on a flat surface. If the Camera Platform has been assembled and installed correctly on the Electronics Chassis you should be able to manually swing the Camera Platform back and forth from its center position, while rotating the Electronics Chassis from side to side, without it contacting the flat surface. If the O rings are contacting the flat surface at any point in the swing of Camera Platform from its center position, then you may have some kind of assembly error in either the Camera Platform or the Electronics Chassis.
Could you possibly provide some pictures of the Controller Board in the WTC and of the Pass-Through End Cap?