This problem is most likely due to the use of Identity fonts in your original PDF files. Identity fonts define each character in the font subset as they are encounterend in the file. Therefore character 1 in the font table might be a "T" and character 2 might be a "H", etc.
Those Identity fonts always come with a conversion table that's stored in the PDF as well so the PDF reader knows how to interpret which character in the table should be represented with which letter/digit. So for instance, instead of the standard ASCII representation (where A=65, B=66, C=67, etc.), that table would contain something like T=1, H=2, E=3, etc.).
That's all fine and dandy until you reprocess that PDF file with Create PDF: the task first converts the incoming PDF to its PostScript equivalent (to be more precise, to a number of EPS pages) which are then merged with your PlanetPress template. But the problem is: PostScript has no mechanism for storing the conversion tables for Identity fonts... so they are lost in the process. And once the task converts the entire stream back to PDF, most of the characters in the font are represented with an index lower than 32, which Acrobat displays as "?".
In such instances, you have two possibilities to workaround the issue:
1 - Modify how the original PDF files are created. Make sure whatever application that generates the PDF doesn't make use of Identity fonts. If you have no control over how that application generates the PDF's, then you'll have to use the second alternative.
2 - Do not map the incoming PDF files to the background of your PlanetPress template. That way, the PDF won't be converted into a series of EPS files (which causes the loss of the conversion tables).
Obviously, if you use Create PDF now, you'll only get a PDF with barcodes on it, and nothing else. But that PDF will contain the exact same number of pages as your input PDF has. So now, you have to PDF files: the original one, and a new one that you are going to "
stamp" over the first one.
To do that, you'd use a script similar to the following:
Set MyOriginalPDF = Watch.GetPDFEditObject
MyOriginalPDF.Open Watch.GetJobFileName, False
MyOriginalPDF.MergeWith "My_Barcoded_Document.pdf"
MyOriginalPDF.Save False
This script
stamps the pages in "My_Barcoded_Document.pdf" (which is presumably the PDF generated by the Create PDF task, and which you stored somewhere) on top of the original PDF (which is the one that contains the Identity fonts).
That should do the trick. And you'll also find that it probably runs faster than your original process did because the entire process of converting the original PDF to EPS and then back to PDF has been eliminated.