I also have this problem and i had my first ride on my brand new Kickr core today. At first i thought it was my gearing so i reindexed my gears, but the problem remained. My bike works fine outside with rear wheel attached.
In the two lowest gears the trainer works Great and is pretty much silent as advertized. This means i can use yhe trainer in ERG mode as Long as im in one of the two lowest gears. However it gradually starts to vibrate and make a lot of noise as i shift into higher gears (smaller cogs). This means that i almost cannot use it in sim mode on Zwift because i have to use higher gears to get some speed and the noise is intolorable.
I have tried everything from fastening my bottom braket and cranks to indexing the gears and realligning my casette (which is brand New) to No effect.
Please write here if you find a solution and i Will do the same.