Illustrator CS4 view doesn't match view of same file in Acrobat

We're seeing a pretty strange problem with Illustrator CS4 (Mac and PC). The problem seems to happen ins CS5 and CS6 as well. We have a complex piece of artwork for a foil blister and we use a paragraph of text that has 3 transforms applied to which effectively step and repeat the paragraph of text in a repeat pattern across the artwork. This setup very precisely as it needs to be 100% accurate for print purposes as several units are printed side by side and the repeat runs across the units. Everything is setup correctly in Illustrator and then we re-save as a PDF with 'Preserve Illustrator Editing Capabilities' on.
We genearally save as a PDF 1.6 but we have tried all the combinations now. The file still looks perfect in Illustrator but when the PDF is opened in Acrobat (any version) the step and repeat (transform) on the paragraph of text is now no longer in alignment on onside of the artwork but still OK on one side. No matter what we do we can't fix this problem andit's recreatable each time. Also it's not file specific as we can build a new file and it will also exhibit the problem. We're only talking about a tiny jump here - <0.2mm but this means the artwork is out of spec. Any help is gratefully received!!!!

Hi Russell
Never a dumb question if it it had pointed us in the right direction. Yes the fonts are all embedded (legally). We tried the Acrobat Preferences but the don't make any difference. If we outline the fonts in Illustrator the problem still happens when we do a save as so it doesn't seem to be a font issue.
regards
Michael

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