Why is my startup script getting a timeout error in FrameMaker?

Using FM 11
ExtendScript
Windows 7
I'm running an ExtendScript from the FM Startup directory, by starting FM from a batch file. The Extendscript opens multiple book files (one at a time) and does a save as pdf for each one. FrameMaker terminates the script with a timeout error at random points in the script after only one or two saves. The Extendscript runs fine when I run it from the FM Scripting window. It only times out when I run it as a startup script. Is there some workaround for this? Sadly, I find no documentation about this.

Thanks, Rick. Here is the body of the Extendscript that is in the FM Startup directory. The batch file starts FM and then this script gets kicked off.
main();
function main() {
    log("Starting the script.");
    var controlFile = File("G:\\fmToPdf\\fmToPdf.control");
    var controlContent = null;
    if(controlFile.exists === true) {
        // Open the file.
        controlFile.open("r"); // r means read only.
        // Read the file contents into a variable.
        controlContent = controlFile.read();
        // Close the file.
        controlFile.close();
    var bookRegEx = /^book="(.*)"/;
    var targetRegEx = /^target="(.*)"/;
    var pathRegEx = /([^\\]+)$/;
    var lines = controlContent.split("\n");
    for (i = 0; i < lines.length; i++) {
        var line = lines[i];
        if (bookRegEx.test(line) === true) {
            var result = line.match(bookRegEx);
            var inBook = result[1];
            var pathComponents = pathRegEx.exec(inBook);
            var fileName = pathComponents[1].replace("book", "pdf");
            for (i = i + 1; i < lines.length; i++) {
                line = lines[i];
                if (targetRegEx.test(line)===true) {
                    result = line.match(targetRegEx);
                    var outBook = result[1] + fileName;
                    log("Starting to generate: " + outBook);
                    fileId = openBook(inBook);
                    saveBook(fileId,outBook);
                    closeBook(fileId);
                    log("Finished with: " + outBook);
                } else {
                    break;
    // close FrameMaker
    Constants.FF_CLOSE_MODIFIED = 1;
    app.Close (Constants.FF_CLOSE_MODIFIED);
    log("We're done.");
    return;   
function openBook(filename)
    var openProp = GetOpenDefaultParams();
    var retParm = new PropVals();
    var BookOpen=Open(filename,openProp,retParm);
    return BookOpen
// save as pdf
function saveBook(file, pdfName)
    var saveProp = GetSaveDefaultParams();
    var i = GetPropIndex(saveProp, Constants.FS_FileType);
    saveProp[i].propVal.ival = Constants.FV_SaveFmtPdf;
    //i = GetPropIndex (saveProp, Constants.FS_DontNotifyAPIClients)
    //saveProp[i].propVal.ival = true;
    var retParmspdf = new PropVals();
    // pdf settings
    file.PDFBookmark = true;
    file.PDFBookmarksOpenLevel = Constants.FV_PDFBookmarksOpenDefaultLevel;
    file.PDFConvertCMYKtoRGB = true;
    file.PDFDistillerAbsent = 0;
    file.PDFJobOption = "High Quality Print";
    file.PDFSeparateFiles = false;
    file.DocIsViewOnly = 1;
    file.Save(pdfName, saveProp, retParmspdf);
    return
// close file
function closeBook(filename)
    filename.Close (Constants.FF_CLOSE_MODIFIED);
function log(message, reset)
    var logfile = File("G:\\fmToPdf\\fmToPdf.log");
    var openMode = (reset === undefined) ? "a" : "w";
    logfile.open(openMode);
    logfile.writeln(getTimeStamp() + " " + message);
    logfile.close();
function getTimeStamp(){
    var d = new Date();
    var timestamp = d.getFullYear() + "." +
                    zeroFill ((d.getMonth() + 1), 2) + "." +
                    zeroFill (d.getDate(), 2) + " " +
                    zeroFill (d.getHours(), 2) + ":" +
                    zeroFill (d.getMinutes(), 2) + ":" +
                    zeroFill (d.getSeconds(), 2);
    return timestamp;
function zeroFill( number, width )
  width -= number.toString().length;
  if ( width > 0 )
    return new Array( width + (/\./.test( number ) ? 2 : 1) ).join( '0' ) + number;
  return number + ""; // always return a string

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