Characters missing in PDF export on Windows

I have a EPS logo placed in InDesign.
When I export to a PDF there are characters missing in the PDF:
When I check the PDF's fonts it lists them as using a custom encoding.
When my collegue uses the same logo in InDesign on a Mac, all the characters are included in the PDF and the fonts are listed as using ANSII encoding.
If we open the logo in Illustrator and export it as an EPS, it works properly on both platforms. However, since we typically place this type of logo via scripting, we would like to be able to either have a fix for the bug or be able to identify the what types of logo files causes this issue so can automatically check the logo before using it. Is this a known problem?

Hmm .. (HelveticaNeue was a likely candidate for the source of your problem if, and only if, the file was made on a Mac -- its system version of HN is a bit ... messed up ... by Apple.)
Just for clarity, can you check with what software this EPS was made? Open it with a regular text editor, that info should be somewhere in the first lines, usually in a line that starts with "%%Creator:".
If you drop the EPS file on Distiller, is the resulting PDF okay?

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