I experienced similar issue when using an reference Vega 64 card as written in Post
#1639 of this thread. the issue seems related to HDCP with specific monitors, because I can see an error message from console every time the stutter happens.
I've not solved this issue, as I returned the card at the end and ordered another MSI AirBoost Vega 56, which is still on the international shipment... After seeing you have the same issue on Vega 56, I have a feeling about I will meet the same issue again with my new card.