This can be caused by various hardware and/or software ailments relating to interrupts. It may be due to bugs but can also happen by nature of certain devices. Running TCP/IP over the parallel port using a large MTU is one good way to provoke this problem. Graphics accelleratorscan also get you here, in which case you should check the interrupt setting of the card first.
A side effect of this problem are dying processes with the message "SIGXCPU exceeded cpu time limit".
For FreeBSD 3.0 and later from Nov 29, 1998 forward: If the problem cannot be fixed otherwise the solution is to set this sysctl variable:
sysctl -w kern.timecounter.method=1
This means a performance impact, but considering the cause of this problem, you probably will not notice. If the problem persists, keep the sysctl set to one and set the "NTIMECOUNTER" option in your kernel to increasingly large values. If by the time you have reached "NTIMECOUNTER=20" the problem isn't solved, interrupts are too hosed on your machine for reliable timekeeping.