Simple vector transparency - printing problems

Morning everybody,
I'm having problems printing a PDF which has been generated from Indesign CS3.  The problem also arises when printing directly from Indesign.  Everything appears OK when on screen.
I have a background colour, in front of which i have placed an Illustrator CS3 file which is a row of white squares with gaps (transparent) between then.  The squares are white, but I really want them to fade from a hue of the background colour to fully transparent.  To achieve this I have used a gradient feather, going from opacity 50% to opacity 0%.  [See sceenshot]
My problem is that all the squares show up when I print the file, even the ones which should have an opacity level of 0%.  On the printout the gradient feather is visible (i.e. the squares 'fade out'), but they do not compeltely fade out to fully transparent. 
Does anyone have any tips? 
Thanks very much for any help with this. 

Thanks a lot for your reply.
I don't have a brilliant understanding of colour, but I believe that all the colours in the document are process [see screenshot].
Turning on overprint preview doesn't change the appearance of the document.  Nor does turning on simulate overprint in acrobat.  In both cases, the appearance of the document on screen is how i want it to print.

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