DON'T USE POSTSCRIPT!
That is the simple and correct answer in short.
- Don't use EPS when you place images.
- Don't use Print when you create PDFs.
PostScript is an old outdated technology from the last millennium.
Use Export to create PDFs.
Use AI, PDF instead of vector EPS.
Use PDF, PDP or even PSD instead of pixel EPS.
PostScript does neither support transparency nor color management.
But I don't see any problem in your log report. But this does not mean that you should post script in any way.
@Jack – you were using a joboptions file by Distiller to convert a PostScript file to a PDF/X-1a.
What you get is no error message, just a report, that everything went ok. And in this case I cannot see any advantage using PDF Export for printing to PostScript/distilling to PDF. Ok, maybe one, CS5 and above would export in a background process.
To prevent InDesign flattening transparency, you could use PDF/X-4 as your export setting. You cannot use writing to PostScript for that task.
Check including tags for tagged export to prevent misalignment of text because of a strange bug with PDF Export when you are using 9pt text on 12pt leading or text with a ratio of 9/12 for point size and leading in multicolumn text frames.