Yes, since your mower floats on the the ground and is behind what the tractor is running over, there is going to be differences in the two U-joint angles.
Take a look at the video and imagine your tractor is one end of the PTO shaft and your mower gearbox is on the other end and see what is causing the vibrations. All you can do is try to minimize those differences when mowing.
Driveshaft Angle and Phasing - YouTube
Take a look at the video and imagine your tractor is one end of the PTO shaft and your mower gearbox is on the other end and see what is causing the vibrations. All you can do is try to minimize those differences when mowing.
Driveshaft Angle and Phasing - YouTube