Loss of Illustration (.AI) quality when converting FrameMaker to PDF

Hello -
We're running into some unpredictable problems when converting a FrameMaker file to PDF. Our images are created in Illustrator (CC), and inserted into FrameMaker (12) as a linked file. In Frame, the illustrations look perfectly fine.
On export to PDF (Acrobat XI), whether "Save as PDF", "Print" to postscript, or "Print" directly to PDF, some illustrations show up "fuzzy" on the screen. It's not the entire graphic, but seemingly random sections of the illustrations that are pixelated. The illustrations are layered, vector, non-outlined .AI files.
Adobe PDF settings (in Distiller XI) are optimized for online viewing.
The reason I'm asking in the Acrobat forum is because if a problematic file is opened in Illustrator, the section that is pixelated in the PDF don't exist as overlays or layers in the AI file. When I say 'don't exist', I mean that if you select each and every layer individually, selections are never the entire pixelated area.
Windows 7
Adobe Illustrator CC
Adobe FrameMaker 12
Acrobat Distiller XI
Thank you so much in advance for your help.

We use structured Framemaker, and insert the graphic as an element. It is a linked file, not imported. The files, as I mentioned, are AI files, not saved as EPS or a rasterized file type. It is a full vector .ai file.
We have occasionally seen a similar problem when there have been overlays (to show dimension/shadows), but removing the overlay has solved the problem. What gets me, now, is that it is creating these seemingly random blocks in the graphics - as though parts of the illustration are being rendered as low-res bitmaps. In the PDF file, we can click on the poorly rendered section, delete it, and it removes a layer or two from the illustration, but the background is still intact (in other words, it doesn't leave a white gap).

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Hello - (This was cross-posted two days ago in the Acrobat forum)
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The explanation I'm seeing is that for FM, it should be saved as .eps, not .pdf. But I also read that importing as .ai simply processes in the same manner as .pdf placement.
We aren't having issues with bloated files by saving as .ai with PDF compatibility turned on, however. And so I can't figure out why for the last 2 versions of FM/AI, this hasn't been an issue. The times we've had problems with the graphics, there have actually been overlays that didn't belong in the .ai file, and once removed, yielded perfectly clear illustrations in the output PDF file (exported from FM).
I'll check to see if we have the same issues with files saved as .PDF or .EPS, which was a work-around we have considered in the department, but one we wanted to avoid, since it means saving 2 of the same file, just in different formats (and may result in updating the .ai and forgetting the "save as" step to the other format, resulting in a linked file not updating).
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Loss of Illustration (.AI) quality when converting FrameMaker to PDF

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