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Without a file to look at, we can't comment :(.

Stick it on your favorite file sharing site - DropBox, Acrobat.com, etc. and post the URL

Thanks - but can I get the PDF that does with it? I need to see the specification of the colors in the PDF to understand the behavior and determine if it is correct or not.

Robert - I am not follow you at all on these things. Can you post some screen shots and sample PDFs that demonstrate these problems.

If you open that file and look at the Fonts info (File->Properties->Fonts), it clearly shows them as native OpenType. I have verified this in the PDF structure. So now we need to see (as I wrote in a separate message) the original PDF to see if they were there to begin with or some other...

It looks like you already ran the flattener on this. I need the original...

Certainly bugs have been fixed and improvements made. So let's see what you've got. The new behavior (ignore) is correct. Separation All is a special thing and should never be converted. Are you seeing this for ALL PDFs or just some? can you post one that demonstrates this problem...

It removes all overprinting instructions and instead creates new objects that are the "final" color.

Just another great reason to move from PDF/X-1a to PDF/X-4

In addition to all the excellent advice already posted, I will make one additional comment based on the old joke. Customer: It never prints right when I use overprinting. Printer: So don't use overprinting. Obviously, getting customers to do the right thing isn't going to happen :(. However...

Yes, if the original files have different values then those values will be carried through in "normal" PDF - we will NOT change it. ONLY IF you create a PDF/X file, will we consolidate the alternative values.

Following my rules in the previous post... IF you tell InDesign to convert colors as part of the export to PDF, then it will do so. IF you are creating a "normal" PDF, then we don't merge or consolidate the spots in any way. IF you are creating a PDF/X file, then we will do whatever we have...

Not really. IF you tell InDesign to color convert things, then it will color convert BOTH object colors AND their alternates. If you tell InDesign to leave things alone, that means both object colors and their alternates. IF you tell InDesign to make a PDF/X compliant file, then it will do so...

Do you mean an actual conversion of Spot->Process/CMYK? OR just a change to the ALTERNATE color associated with the spot? The former will NEVER happen in our products UNLESS you explicitly choose to do it (via the Ink Manager, Color Convert, Preflight, etc.) The latter CAN HAPPEN if you are...

AFAIK, the spots in placed PDFs (or EPSs) are NOT remapped during "normal" PDF export - they would be left alone. So if you had CMYK-based alternates in the original and then exported, you would still have CMYK-based alternates. Also, if you have different spots of the same name, they will...

No, Acrobat won't reopen those (or other) windows automatically.

Both PDF and EPS/PS have a concept called an "alternate colorspace". For spot colors (technically, the Separation colorspace), an alternate is provided for when the viewer does not have the original present. The obvious example being Adobe Reader, which knows NOTHING about Pantone inks - so it...

Clearly HOW you are producing the PDF is an issue, since at least one of the fonts you have in that screen shot is NOT embedded - certainly not what you want. That's to be expected, since when producing a PDF using certain methods, a CFF-based OpenType font will be "reduced" to it's original...

People also jump off bridges - but I'm not going to help them do it :).

Correct. Pantone provides Adobe with a library that our applications use. That library includes both Lab as well as CMYK values for each of the provided colors. As the actual inks that Pantone produces changes, and as they improve their colorimetric measurements, those Lab & CMYK values...