Ok, found something in "Show Current CPU Usage". It's for the big sites account, and is taking 60% of all resources as it seems:
/usr/local/cpanel/3rdparty/bin/analog +CIMAGEDIR /images/ +CDOMAINSFILE /usr/local/cpanel/3rdparty/share/analog/lang/usdom.tab +CCHARTDIR ./ +CALLCHART ON +CLANGFILE /usr/local/cpanel/3rdparty/share/analog/lang/us.lng +COUTFILE /home/kim/tmp/analog/example.kim.example.net/7.html +CLOCALCHARTDIR /home/kim/tmp/analog/example.kim.example.net/ +CCACHEOUTFILE /home/kim/tmp/analog/example.kim.example.net/cache.out +CCACHEFILE /home/kim/tmp/analog/example.kim.example.net/cache +CVHOST ON +COSREP ON +CBROWSER ON +CFULLBROWSER ON +CREDIRREF ON +CREFSITE ON +CFAILREF ON +CLOGFORMAT COMBINED +CHOSTNAME example.kim.example.net +CHOSTURL
http://example.kim.example.net/ /usr/local/apache/domlogs/example.kim.example.net
Killed this process and everything went back to normal. So this process is the problem. Now the question is how to stop it from happening again. Tried to disable it under "Statistics Software Configuration", but it seems to be running anyway.
Is it enough to deselect "Enabled by Default" and "Active" on all Statistic Softwares under "Statistics Software Configuration" to disable all Statistic?