PDF scanned by Epson v. Canon annotate by PDFPen (not) viewable in Preview

My question relates to the applications PDPen and Preview, and the scanners and scanning software of Epson and Canon.
When I had an Epson print-scan-copy machine, I would scan originals into multi-page PDF files and I would page-number and annotate these using PDFPen. Subsequently, I could and would use Preview to look at these files and also print them (all page-numbering and annotations created through PDFPen would be visible in Preview, as one would expect). Now I have a Canon print-scan-copy machine. When I scan in multi-page PDFs using Canon's scanner/scanning software, I was surprised to find that page-numbering and annotations in PDFPen are invisible in Preview – Preview just doesn't 'see' them. Naturally, when printing these PDFs through Preview, page-numbers and annotations created through PDFPen don't print either. When you re-open the file in PDFPen, they are there all right.
I scanned in PDF's using both, Canon's Navigator app and also by way of 'Open Scanner Driver', and also tried to fiddle with a setting or two. But the above problem persists. Can someone explain this problem and also tell me which setting to change either in Canon's Navigator or after going into 'Open Scanner Driver' so that the PDF files it creates can be page-numbered and annotated in PDFPen with the final result being recognizable to, and viewable in, Preview?
Thanks.

I'd say it has something to do with the pdf characteristics produced by the two sets of scanning software since that's the underlying difference in your setups. This question really requires familiarity with the third party Canon software, and then somebody who also uses PDFpen. I recommend you at least try the Canon support site [http://www.usa.canon.com/consumer/controller?act=SupportIndexAct] and see if they can describe the characteristics of the PDF.
Although Preview isn't a bad application it doesn't have all the feature support functionality that Adobe Reader has. I much prefer Preview but once you get beyond the truly basic PDF (i.e., you have started modifying it with PDFpen) it may require a PDF browser such as Reader to get all the features. In this case the CanonPDF has added just enough difference to cause the modified PDF to no longer work.

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dell1600n_net
dmc
epjitsu
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genesys
gt68xx
hp
hp3900
hpsj5s
hp3500
hp4200
hp5400
hp5590
hpljm1005
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ibm
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lexmark
ma1509
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microtek2
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nec
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pie
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# Copyright (C) 2004 Olaf Meeuwissen
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#scsi EPSON
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# For all USB scanners that are officially supported by this backend,
# this presumption is true. A list of such scanners can be found in
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usb 0x4b8 0x83f
# For any USB scanner not known to the backend (yet), you may, at your
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# You can do so by the following configuration command:
# usb <USB vendor ID> <USB product ID>
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usb /dev/usb/scanner0
usb /dev/usbscanner0
usb /dev/uscanner0
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#pio 0x378
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# by sane-desc 3.3 from sane-backends 1.0.19 on Fri Mar 7 06:29:43 2008
# udev rules file for supported USB devices
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# EPSON Stylus CX4300 | EPSON Stylus CX4400 | EPSON Stylus CX5500
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LABEL="libsane_rules_end"
Can anyone help with this?

Almost solved.
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