I have a set of BK 5001 servos connected to my Spirit 2 for the cyclic of my new Synergy 516. If I set the frequency to 50 or 60hz they are very smooth and quiet. If I set the frequency to 333hz they are very loud and make a grinding noise. The Spirit 2 is connected to a Futaba R3004SB receiver via S.Bus2 and my transmitter is a 18SZ. If I connect the servos direct to the receiver they are smooth and quiet.

Here's a video of them at 333hz.

https://youtu.be/duX3L4LSFeU

Is there something wrong with the servos? Is there something wrong with my Spirit 2 setup? Is it safe to fly this way?

There is nothing wrong.
It is just because your receiver is transmitting data slower than the servos can react.
So servos are displaying what is just happening.
The only solution is to make data from radio to receiver faster. It might be improved with other futaba modulation that can transmit data faster.

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Spirit System developer

I tried using a r7008sb receiver this morning which runs FASSTest protocol. The results were exactly the same. Should I reduce the frequency rate from 333 to something lower?

FASSTest protocol might run at the very same frequency. Rather try to set just 7CH transmission, since MULT is slower.

The issue is actually not a problem at all. It is actually doing what it should. With the faster servos it will be more apparent. This is why lower frequency makes the problem invisible. 200 - 333Hz is correct settings.

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Spirit System developer