I take you're using Linux server?
Your problem is probably in your hardware, namely your hard disk.
In Windows, the drive gets fragmented. to a point where I had to buy a second party de-fragmenter ("PerfectDisk") and schedule daily de-frags.
Zones will start to crash with little fragmentation, so de-frag, regardless.
Swap drives get fragmented too.
Not sure what happens to Linux, but a Linux swap drive on the same hard disk will slow you down.
100+ static zones on your server will cause zone crashes if your hard disks are not properly tweaked, or are just too slow.
Maybe your hard disk is getting old and slow. Try adding a second hard disk and move your Linux swap partition there there (in Windows, just move the swap file to the new HD).
I've had these problems under both Windows and Linux and have solved them by tweaking the hard disks. Took me all these years to realize this.
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