I keep getting the can't keep up message when more than 1 player is on. And traveling by boat is impossible. You suddenly hit land like the server can't keep track on your location.

[Server thread/WARN]: Can't keep up! Did the system time change, or is the server overloaded? Running 10379ms behind, skipping 207 tick(s)

I've checked the server when the message appears, none of the cores on the cpu reaches 100%, there's plenty of ram available and the disk read/write activity got loads of capacity. The server should be good enough to run this.

I started running it on a vmware server, with 4 cores and 6GB ram. I've tried running it on Ubuntu, and finally I moved it to a standalone server where it's running now. Nothing helped.