If you don't have a way to sync it to an external source, you're going to just have to deal with it. There is nothing in the configs you will be able to change. When you don't have any other systems to sync from, and you don't have any external time sources, Netware will get it's time from the hardware clock. Again, a highly unreliable source despite what you say.
The one thing that I could recommend.. Go into the BIOS. make sure the time is set correctly there. Then boot to a DOS prompt, and see if it's set the same. It might not be and this could contribute to your problem. Set it correctly from DOS if necessary.. Then, boot the server and check the time from the console and verify that it's the same as what you did in the previous steps. Not an optimal solution but you don't have much other choice.