Thanks for sharing the file with us. We analyzed the file at our end and it seems its not a valid PDF/X-4 file due to the issues with an inconsistency between glyph width information in the PDF and the embedded font.
You may try regenerating a new pdf file using original .AI file with a newer version of Illustrator as the CS6 version of Illustrator is quite old and it is possible that newer Illustrator versions can fix this issue.
Also, both version of Acrobat- XI and DC showing different results when preflight analysis is done as with each version of Acrobat Pro DC has improved versions of Preflight that may find problems that were not previously diagnosed.
Thanks,
Shivam