In theory, if you take the exact same InDesign document that you have on a Mac and then migrate the source documents and resources over to a Windows-based system running the same version of InDesign, the PDF files generated from the Windows-based system should match exactly the PDF files generated on the Mac.
The PDF creation capabilities of InDesign (and for that matter Illustrator and Photoshop as well) are not dependent upon any operating system services, but rather Adobe-developed libraries which are effectively identical between platforms. The only difference that might be seen in the resultant PDF files might be metadata indicating which platform InDesign was running on.
Note that I included resources in my first statement above. If there are any differences between the font, ICC color profile, and PDF option files that you using on Windows versus Mac, yes, you could conceivably see differences although such differences should generally not cause “failures” as you describe them. Exactly what type of failures are you experiencing? RIP crashes, diagnostic error messages and premature job termination, color issues, graphics anomalies (such as transparency issues)?
How “ancient” is “ancient” in terms of the Apogee that you are using? Why are you even using that intermediate step?
Do the files from both platforms for the same original InDesign documents display correctly on screen? If you run Preflight (either the built-in preflight in Acrobat, which is actually Callas, or other third party preflight plug-ins such as PitStop), do you get any different diagnostics between the files from the different platforms?
If you do a compare of the resultant PDF files from the same InDesign document from both Mac and Windows systems, what differences do you think you actually see? Have you even run the resultant PDF files from both platforms through software to show the actual differences?
How are the PDF files generated by InDesign being transmitted to the Apogee? Some utility program provided for the Apogee? Sneakernet? FTP or similar protocols? Sometimes these programs try to be “clever” and improperly muck around with CR, LF, and CR/LF line ending characters or for that matter with any non-ASCII character.
For what it is worth, from the time of the early InDesign 1.0 prereleases until current times (over 20-something years), I never saw cross-platform issues in terms of the actual PDF or for that matter PostScript generation from this software and I've used both platforms for development, testing, and production purposes (i.e., I'm a fanboy of neither Apple nor Microsoft).
- Dov