Sorry to revive an oldish thread. I have a very similar problem and have been reading up on this all day. But am not clear if there's anything I can do or if it's actually the printer's responsibility.
In my case it's a one colour (black/greyscale) job and the boxes aren't thin white lines but a whole box shape making the % fill background slightly lighter when a drop shadowed object is over it. The object is angled and the box shape covers the whole area of the angled picture (i.e. square on, not angled). It's presumably the same issue, i.e. drop shadow/transparency and the software's ability to flatten or deal with it. But I can't figure if I should be going up a level or down a level when creating the pdf (i.e. to 1.4, 5 or 6?) and thus leave the transparency live or not.
The printer has Acrobat 7 and uses FlowDrive and CTP technology. I did my layout in InDesign 3.0 and saved the original problem pdf as 1.4, I think. The problem is totally invisible in InD and Acrobat at any %. Even with Overprint preview on. It only appeared on the plate (or in fact its preview). Can I get the printer to change settings on his software to get past the problem? Communication is slow because they're in a different country. And time is getting short.
If I can't solve it I'm going to have to go through and remove every drop shadow (and in spite of previous discussions on their being a blight on the face of graphic design, I'd quite like to keep them!)
Any help appreciated. Thanks very much.