That can be many things, but here are a few examples.
- High harvest multiplier without individually specified multipliers (per resource) or optimised harvesting.
- Someone travelling in to the server with many engrams/items etc.
- Transferring large amounts of resources from/to dedicated storage (more of a problem with S+ and derivatives since they store so much more).
Try to monitor the Server FPS with
SetCheatPlayer True as admin to see if the server FPS is dropping when the desync/rubberbanding occurs.