IDCS4 preflight errors regarding resolution in .eps files from Illustrator

We have been having real problems with some (but not all) .eps files (both supplied and created in-house) in IDCS4. When viewed in Illustrator, the images are fine, but after the images have been imported into IDCS4, the problems begin. There is nothing obvious that is the same across all the images that IDCS4 has a problem with, apart from gradient fills.
Indesign's Preflight reports that the EPS files are below 300dpi. When we changed the 'display performance' of the images to 'high quality display', we could definately see parts of the image had become pixelated, despite the image being composed entirely of vectors.
We've tried resaving the images as .eps from Illustrator CS2, CS4, etc, and as .AI files, but to no avail. We can only presume that IDCS4 is causing this issue, as having resaved in all these different formats has provided no answers. The images have trasnpanrecy set to high res, the document raster effects settings is set to 300dpi.
This is repeatable on multiple Macs, running OSX 10.4 & 10.5. The only fix I have found is to enlarge Images in Illustrator, and scale them down in IDCS4
Any ideas anyone?

**UPDATE**
I have found that If I wrote out the images as .AI files from Illustrator CS2 (Not CS4 or CS4 saving as a CS2 file), the resulting AI file works OK.
This is no real solution though, and .EPS files allow for embedding the fonts and .AI files don't.
Tried creating extremely high-res transparency profiles, etc. Problem persists.

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