Here's my whole code if it helps. I'm wondering if the script is moving too fast. I think that the first files are still PDFing while the others are opening and closing. Could that be it? I'm not sure why else the for loop for the PDFing is only working on the first file.
var myFolder = Folder.selectDialog("Select Input Folder");
var myIndsnFiles = myFolder.getFiles("*.indd");
var exportPath=Folder("/").selectDlg("Select PDF output folder:");
var pdfPreset = "Press Quality";
for(k=0; k<myIndsnFiles.length; k++)
{
app.open(myIndsnFiles[k]);
var jobNumber = "12345";
for (aPage=0; aPage < app.activeDocument.pages.length; aPage++)
{
app.pdfExportPreferences.pageRange = app.activeDocument.pages[aPage].name;
app.activeDocument.exportFile (ExportFormat.PDF_TYPE, File(exportPath+"/"+jobNumber+"_"+pad(app.activeDocument.pages[aPage] .name)+".pdf"), false, pdfPreset);
function pad (n) {
return ("00000"+n).slice(-3);
}
}
app.activeDocument.close();
}