Mysterious lines in PDF

So any help would be useful.
At our shop we use CS3. Usually when creating our artwork for print we use this work flow:
1. Flatten transparency
2. Save as .EPS
3. Distillation (PDF/X-1a;2001)
This creates small, strange, artifact looking lines throughout the document. These do not print and if you zoom in on them in acrobat they disappear which would lead one to assume that they do no exist. Recently we had a printer claiming that they printed out and I need to find a way to circumvent these 'mysterious lines'. They also cause a lot of problems with clients.
So any help, info, input would be helpful because i cannot find any record of this particular thing occurring.
IM: [email protected]

I agreed with eja34. if we have versio above 4 then there is no issue.
ISO FILE

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