I can think of two possibilities.
(the simple ones)
-A damaged/unbalanced shaft or U-joint is going.
(I have a joint going on mine and it makes 'knocking' type noises when I lift my blower up high with the 3-pt)
-The lock bolt that locks the PTO shifter onto the shift shaft has slipped out of place (or the dedent is a bit worn).
If that is the case (trial and error) loosten the lock bolt and reposition the shift arm.
It could be that while you believe that you are in 540 rpm you actually have most of 540 but are also catching a bit of the higher or lower gear as well.
To check that out , while pto is engaged and running gently move the shift lever back and forth just a little bit and see if the noise stops.
The distance you moved to stop the noise would then be the amount of correction you need to make in the opposite direction.
This also occured on mine.
Good luck!