I have a weird situation, and I'm thinking it's related to the particular font, not anything in InDesign, per se.
I have some black type with a tiny (.05pt) stroke applied in ID (CS5.5). Everything looks fine on screen. However when I export a PDF, the type doesn't align with the strokes — it's as if different kerning/tracking has been applied to the type, but not the strokes. It's not all the type, and not on every line, but most of it has this "ghosting" or "halo" look to it when you zoom in to the PDF.
We've run similar type treatments in different fonts, and this didn't happen. I've tried a variety of PDF export settings (Press Quality, PDF/X-4, 1a) even exporting to IDML and bringing it into CS4. I'm not changing the fonts to outlines (I've read threads about how outlined text w/strokes caused issues) and there is no transparency. (As a test, I did try Isolate Blending and flattening, but that rastered all the type into jaggy bitmaps.)
There's also something I haven't normally seen (because I don't normally look) but it looks like the font is listed twice in the Fonts list in the Document settings — once ansi encoded and once again with Custom encoding.
This is what makes me think it's the font.
This is how it appears in Acrobat X:
The font is Cochin LT Std (OT) Roman. This is how it's listed as an embedded font in the PDF:
For what it's worth, because it may be related, I've seen weirdness with some fonts when rendered in a PDF before. Sometimes it appears if the type is improperly kerned. (We started seeing that, rarely, when we moved to CS5 from 4 and started using PDF/X-4 instead of 1a.) I've actually seen it on occasion where the letters transpose, as if there were negative kerning amounts in the hundreds applied, the letters appearing on top of each other and in different order. (CS2 & 3)
All these instances look as they should in InDesign, but the aberrations appear in the PDF (typically viewed in Acrobat, but also visible in Illustrator and Preview).
Further testing suggests that the stroke and type are rendered independently of each other. If I open the PDF in Illustrator, I need the font installed for the type to render properly. However if I turn the font off, the type is rendered in a substitute font but the strokes are not — they are still rendered as outlines in the shape of the original glyphs.
and yes, it appears only in this font with this styling. If I create a different style with the same font, I don't get this aberration. If I apply this styling to different text, I get the same effect.
You can either post a link here for anyone, or send me a private message. I have Cochin LT Std, but a newer version, which might be instuctive, too.
I'm not surprised, by the way that the sroke is a separate object in the PDF. I'm not sure how it could be anything else.