I am getting a message in my server console that reads:

17.01 11:46:33 [Server] Server thread/WARN Can't keep up! Did the system time change, or is the server overloaded? Running 3171ms behind, skipping 63 tick(s)
17.01 11:56:15 [Server] INFO Jan 17, 2018 11:56:15 AM io.netty.util.ResourceLeakDetector reportUntracedLeak
17.01 11:56:15 [Server] INFO SEVERE: LEAK: ByteBuf.release() was not called before it's garbage-collected. Enable advanced leak reporting to find out where the leak occurred. To enable advanced leak reporting, specify the JVM option '-Dio.netty.leakDetection.level=advanced' or call ResourceLeakDetector.setLevel() See http://netty.io/wiki/reference-counted-objects.html for more information.
17.01 12:02:03 [Server] Server thread/WARN Can't keep up! Did the system time change, or is the server overloaded? Running 2970ms behind, skipping 59 tick(s)

On top of this and likely unrelated, when I go into a Lesser Shogoth cave/spawner area the shogoths are standing still and not moving/reacting. When I look at them it states Waiting for server... and I cannot hurt/hit them at all but when I look away or at anything else I don't get this notice.

I would recommend upgrading your server to the latest version which is v5.7b and let us know if it persists.

Sounds good. Thanks.