Flattening Transparencies - Gimp, Scribus, and DriveThruRPG

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I used Scribus to create a black and white PDF, including images prepared with Gimp. I submitted the PDF to DriveThruRPG for their print on demand service and it was initially rejected by their printer (Lightning Source). This was the feedback from DriveThruRPG:

the interior file had some PDF/X compliance issues. They ran it through preflight, flattening transparencies, and the resulting file worked.

For next time, how do I fix this problem on my end? Here is the workflow that I used:

  • I received images from various sources, opened them in Gimp, converted them to grayscale, and saved them in EPS format. None of the images contained any transparency that I am aware of. Most of the images consisted of black line art on a white background.
  • In Scribus I created a document, set the Color to Grayscale, laid out the text, imported the EPS images that I had created with Gimp, and exported the document with Compatibility set to PDF/X-1a.

What would it mean to "flatten transparencies" and at what point in the process would I do that? In Gimp? In Scribus?

Edit:

Okay I see that GIMP has a Flatten Image command which removes the alpha channel. Should I try running that on all of the images before saving them in EPS format?

Could Scribus also be introducing transparency into the PDF somewhere? At this link... Is there a way to flatten a .pdf image from the command line? ...I see this command:

pdf2ps orig.pdf - | ps2pdf - flattened.pdf

Should I also run that on the PDF before sending it to the printer?

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