I am encountering following problem. There is one server (DL160 G5) running Centos 6.3 with default kernel 2.6.32-220.2.1.el6.x86_64 - at this point I'd like to add that issue appeared also at older version - 6.1 and older kernel (do not remember exactly which version). There is cPanel installed and from time to time it becomes unavailable (network connection). What I've checked is (via KVMoIP):

• load average is completely normal
• it does not lack memory or disk space when problem occurs
• no console notifications
• checked all access logs and there is no sign that it can be caused by a client script
• cannot even access local interface (127.0.0.1) or main IP address
• running tcpdump I can only see packets arriving to server - no responses
• all services seem to be running properly (mail,sql,http,ssh)
• checked crontab and all clients' crontabs too
• network port utilisation is low ( up to several Mbits)
• arriving packet rate is low - hundreds per second (according to tcpdump)
• console (via kvmoip) works fine, no lags
• there is no conntrack at this server
• there is no ipv6 at this server
• flushing iptables, unloading modules does not resolve problem
• restarting network does not resolve problem, no errors appear
• it also occurs when two sepearate networks are configured (and multiple gateways) as well as one IP, one default gw and one network is configured - so it seems network configuration independent
• it seems to repeat randomly (load,packet rate,bandwith usage,load independent)
• checked server with different rootkit detection tools - it seems to be clean
• server has been rebooted, it did not change anything
• there are no interface errors
• it apperas randomly can be once a week or several times per day

It usually works fine after 1-15 minutes. What I can also check? It is definitely OS issue - there is traffic at interface only in one direction when problem occurs, can not even ping loopback. Any ideas? Recommended checks? Anything I did not checked above.