Or maybe this is a job for creating a PDF Export Preset? I've created a basic preset with the PDF/X1a:2001 standard but left all the default settings. I'm not sure what to change that may help?
Thanks in advance!
You could use [High Quality Print] pdfexportpreset to generate a good quality pdf. You can play around with different pdf export presets present in Indesign to see which one outputs the result that suits your requirement, or create a new preset.
Hope this helps
You must have flattening there.
If that's the case, you have two options:
1) You can export to PDF/X-4 which preserves transparency (advisable).
2) You can specifiy a high quality transparency flattener setting.
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