Transparency problems: Objects not printing

Recently had 2 jobs go bad due to objects with transparency effect applied not printing when export to PDF was created (both from CS3 and 4 and 5). I could not find anything special about the files, and I could not reproduce the problem (unless I copied an object into the same box with the original object).
But files coming in from 2 different customers had this issue:
The PDF made from Export to PDF produced a PDF that looked as if it did not print the object with transparency effect, but upon further looking the objects were there, but to get them to show (and print) we had to delete a box (nothing in the box) using Pitstop, then the object would show. The Transparency was correct and overprinting was correct, but the original PDF produced, had them covered with this box. If I made a flattened PDF(1.3) then the objects would show and print fine.
Has anyone had a simlar problem? What is the print shop production environment solution?
Thanks
Willy

Funny, just today I came to similar problem. Creating pdfs for clients approval: a preset that I user regulary (with downsampling etc) creates pdf with this problem, and the press preset creates correct pdf. I guess that it has to be a picture box property... but can't think of any solution other than cutting the content (picture), creating new box and pasteing it into.

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