How to standardize image quality?

I am working in an INDD (CS 5.5) file and have placed into it EPS graphics that use layers of color at various transparencies. I embedded all the EPS links into this INDD file, then exported it as a PDF. The AI (CS4) file in which I created the graphics, the INDD file, and the PDF (CS5.5) are all in CMYK mode. For some reason, some of the images in the PDF appear washed out, with small dots at various edges of the image. I'm stumped--any ideas as to what the root problem could be?

Asley,
in addition to John's comment:
EPS doesn't ever contain layers with variable transparency (besides ordinary
transparency in areas, where no objects are placed).
Exporting AI files as EPS results in flattening. This is not generally wrong,
but it should be done deliberately.
For your workflow it's probably recommended to use AI files in ID.
A very different question is then, whether the ID file should be flattenened,
exporting as PDF. In my opinion it's recommended, because the result can
be checked by you. Flattening at RIP level may cause shifts which are not
under your control.
I'm aware of the cheap advice 'if your printer is not able to handle Adobe files
with live transparency correctly, the find a better one'.
By the way: I'm using regularly EPS for graphics which are programmed
directly in the programming language PostScript.
Best regards --Gernot Hoffmann

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