I'm not sure who makes the Frontier for JD. My Land Pride has a slight vibration as it's coming up to speed, more of a shudder than anything else as it accelerates. Once it's up to speed it's as smooth as anything with pivoting blades can be.
If you're getting a whine it's probably the gearbox if the pressure angles and contact points aren't right.
I'd look at it this way. Before the dealer returns the unit to you, listen to it running at their shop. If the noise is still there, there is either a problem with that particular unit, or it's the nature of the beast. Either way you're not going to be happy with it. There's a slight chance it may be the combination of that cutter and your tractor.
The worst of it is, you may be able to return this one, get something different altogether and have the same noise issue.
Listen to them run it, if they say "That's normal.." you have a decision to make, and not an easy one.
Chilly