I have noticed this phenomenon for quite some time. Just thought I might want to share this:

QUOTE
After doing a Graceful Reboot from WHM, you wait for 15 minutes and check on the WHM's Server Status page. You get all the green light. None is red.

This doesn't mean that the server is working properly. It has happened to me many times that, under this condition, the server was acting funny:

You might see these:
- Some sites can be accessed while some give you DNS errors.
- Emails are not delivered but placed in the queue.
- The cPanel/WHM News page of WHM (i.e., the main page of WHM) cannot be loaded. A line of error is printed.

To solve the problems, simply go to WHM and do the service restart manually one by one, with BIND being the most important. In fact now I will do this EVERYTIME after I reboot my server, whether or not I notice any error.

Now look into MRTG. You will see that your server was down earlier.