These issues are related to file creation.
Since the file is created from the third party source, sadly there is not much that can be done.
On the contrary many things can be done.
I see, "Acrobat Distiller" is a third party product ;-)
But the actual problem is not the document creation but the signature creation which was done with PdfBox. PdfBox is an OpenSource project and thus it can be easily addressed there. For that I needed to know where the PDF spec violation was. After a bit of research it turned out that the signature is using an reference dictionary. Since the document itself is PDF 1.4 and the reference dictionary has been added in 1.5 preflight complains about it.
Acrobat Distiller is not third party product, it is the engine of Adobe Acrobat.
Thank you for sharing your findings, I really appreciate this.
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The "Application" meta data information is set to "PDFBox", so that's why Tariq was very likely referring to the 3rd party software. The PDF file you linked to is actually not the one that you've used to create the screen shot.
Regarding the PDFBox introduced problem, you may want to post your findings on the PDFBox "Users" mailing list: Apache PDFBox | Mailing Lists
It may not be the exact same PDF however the error is exactly the same... So for the problem at hand perfect for analysis...