One possible culprit is overall memory usage – forcing the server to start swapping. If this is coupled with a close-to-full disk and a fragmented paging file. I’ve seen this cause up to 8-10 second delays on a Win2K server.
Another possibility is a hard disk that is starting to die. Check the event logs for any signs of trouble that way. Although this seems less likely.
In cases like this, I always start with checking disk use, memory usage, event logs for anything that might correlate.
Good luck, and let us know what you find.