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I wont blame Nagios at any cost. I was using it more than 3 years and It was working fine till now which proves its stability itself.
Finally I reinstalled Nagios version 4.1.1 on another machine and its started working as normal. which means something wrong with system itself (OS/Kernel). I tried almost all ways,all scenarios on my old machine in past 3 days which I could do, Last option left for me is to reboot machine , but as this is Production machine i changed my mind.
I am thankful to this Forum and special thanks to jdalrymple who helped me to resolve this issue.