It's not uncommon for many bushhogs to cause some small amount of vibration, but the question is how "bad" is your vibration? Possibly you have a blade imbalance that generates a vibration at or above a certain rpm (frequency), or the PTO driveshaft itself can also cause a vibration. If you have a stumpjumper that the blades are attached to, that could also be bent or warped and cause a vibration. Have you tried raising the BH up and watching the blades and pan while slowly rotating them by hand? WARNING: IF you do that, MAKE SURE you have the bush hog blocked up with jackstands so there is no chance of it falling on you!
Sometimes the blades (which are made to pivot) will rotate such that when it stops they will sort of fold back on each other and get wedged together. This will cause a LOT of vibration as soon as it starts to spin up though. You will know that right away, but it doesn't sound like this is your problem.
If you know someone with a PTO shaft of the same length and ends as yours, you could swap just to try and see if that makes a difference. (If you try that, make sure their tractor doesn't have a similar vibration so that it's a valid experiment). Good luck.