Ok, I answering to my own problem now.
Thank lord manage to get the issue fixed.
So FYI to everyone who get segfault issue on FC8 or equivalent, the root caused of the problem is because your ISPConfig config file is not properly setup. Example in my case DNS Zone file is pointed in wrong folder.
So the solution to this is to change some permission, restart named and re-edit the DNS settings and magically it get saved this time.
Here is the step
1. Change permission on named, just to make sure permission is in place
chmod 755 /var/named/
chmod 775 /var/named/chroot/
chmod 775 /var/named/chroot/var/
chmod 775 /var/named/chroot/var/named/
chmod 775 /var/named/chroot/var/run/
chmod 777 /var/named/chroot/var/run/named/
2. Restart named service to take effects on the permission changes (if any)
3. Go to Management -> Server -> Settings -> DNS, Zonefiles Dir. and change the setting to :
As for now, no more segfault issue and my web server is back to working condition.
P/s : Still I'm curious how my Zonefile settings somehow change it self, either because of ISPConfig upgrade ? Maybe FC users out there can share if you face the same problem.