Ok, ignore that...I found my answer.

Apparently ADODB.Stream for reading the file is terrible in this code.

This worked much much much better:

function ansiToUtf8(fileName) {

var indir = "ansiin";

var outdir = "utf8out";

var ansi = WScript.CreateObject("Scripting.FileSystemObject");

var utf8 = WScript.CreateObject("ADODB.Stream");

utf8.Open();

utf8.Charset = "UTF-8";

utf8.WriteText(ansi.OpentextFile(indir+"\\"+fileName,1,false,false).ReadAll());

utf8.SaveToFile(outdir+"\\"+fileName, 2 /*adSaveCreateOverWrite*/);

utf8.Close();

}