1.8: Can't keep up! Did the system time change, or is the server overloaded?

[10:47:20] [Server thread/WARN]: Can't keep up! Did the system time change, or is the server overloaded? Running 3399ms behind, skipping 67 tick(s)
[17:09:05] [Server thread/WARN]: Can't keep up! Did the system time change, or is the server overloaded? Running 5984ms behind, skipping 119 tick(s)
[06:00:06] [Server thread/WARN]: Can't keep up! Did the system time change, or is the server overloaded? Running 3651ms behind, skipping 73 tick(s)

There's no one logged in with the above messages, and the server is practically idle. This happens during game play as well but the fact it's happening with no one logged in has me thinking it might be a bug.

Not to mention this didn't happen with older versions.