You should check:
- active udp connections
- rootkits
- phpshells and malware
Code:
clamscan -r /var/www/
There are many reasons. An user is using a phpshell,cgi, someone found a exploit in a plugin/code, a successful bruteforce attack to gain access to your system...I don't know, there are many situations
Do you allow cgi for your sites?Are you using fcgi+suexec?Do you disabled some php functions?Are you using suhosin?
Also check for unusual high cpu/processes!
Cheers!
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