Why do different pdf output formats produce different visible plot file content?
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A PDF plot file type PDF/A has removed certain drawn entities when plotting from AutoCAD but set differently does not.
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It is not inherent in the format. Maybe you can ask AutoCAD why they do that.
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Thank you for your comment. the DWG to PDF plot device from AutoCAD is correct consistently. As the requirement is text searchable PDF's and the standard stipulates the use of shx fonts rather than TTF we have been forced to purchase adobe DC to accomplish this. 95% of the time the results are as required.
With the PDFMAcad.arx program added to AutoCAD 2014, the PDF (create PDF) command produces text searchable PDF plot files, but if text masking, or wipeouts have been used a black square is plotted, obscuring everything else. This is a common problem we have come to expect.
The problem above addressed 22 blocks inserted in a drawing 21 of which did not plot. Changing from PDF/A format printed all 22. AutoCAD did not do that.
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Ok, PDFMAcad.arx seems to be part of Acrobat. What version of Acrobat Pro is it?
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I am running Acrobat DC
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Ok I don't know why it happens but I may have a work-around. Make a non-PDF/A file. Is it correct? Ok, now open it in Acrobat and save as PDF/A (or use Preflight for more conversion options). Is it still correct? This should be ok unless you need tagging.
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Setting the options as below appears to be allowing the correct production of PDF plots from AutoCAD.
Opening each in acrobat and saving a second time is not practical as it will more than double the time need to perform this operation.
I will need to find a method of reporting this direct to Adobe so a bug fix can be implemented.

