Yes, you are right, if you do not "ARES" a PDF the barcode should still work but what you may see is that the Barcode gets encrypted. When the barcode is encrypted some of the space of the barcode is used up by the encryption process. So, this may cause a barcode that is filled to capacity perfectly fine in Acrobat to gray-out in Reader.
I'm having a similar problem with barcoded forms developed in Designer ES 8.1:
The barcodes don't show in Adobe Reader 8.1.0 - any barcode just
appears as grey area, whereas they run ok in Adobe Reader 8.0.0.
System is Windows (XP or 2000/2003 Server).
Thanks for any help. If needed I can provide the pdf/xdp.