This line automatically generated is causing the problem:
$CKEditor_config["docType"] = "<" ."!" ."DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">";
Use this one and it works as expected:
$CKEditor_config["docType"] = "<" ."!" ."DOCTYPE html PUBLIC \"-//W3C//DTD XHTML 1.0 Transitional//EN\" \"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd\">";
IF we escape the quotes like this it works:
$CKEditor_config["docType"] = "<" ."!" ."DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01 Transitional//EN\" \"http://www.w3.org/TR/html4/loose.dtd\">";