Indesign CS4 to PDF 1.3 transparency issue

Question

We submitted an ad to the local newspaper that we created in Indesign CS4 and Acrobat 9. The ad was exported as a press-quality Acrobat 4 PDF.
It is a fairly simple layout, with type and a logo.
The headline and logo have a drop shadow applied with multiply blend mode. All colors are CMYK.
When the ad prints, the headline and logo have 1% black-filled boxes around them.
I know this is a transparency issue. However, we've done the same ad in Indesign CS3 and Acrobat 8 with no problems as long as we were CMYK and Acrobat 4.
Has something changed in CS4 that I don't know about? Could it be the multiply blend mode rather than normal?
Problem is, the newspaper can't give me a proof -- we have to wait and see what happens when they print. I can't simulate the problem on my end. The ad prints perfectly on my HP5000N in b/w and on my Phaser 8560 in color.
One workaround suggested was to export the file as a JPG or EPS and save as a Photoshop PDF. We did that on one ad that will run Monday, so we'll see. However, that makes the files with photos enormous -- like from 4 mb to 26 mb.
Any ideas would be greatly appreciated. We're in the middle of an ad campaign and we're resorted to the old-fashioned manual drop shadow out of desperation!
mev

Answer 1

Has something changed in CS4 that I don't know about? Could it be the multiply blend mode rather than normal?
Something did change. In some cases (maybe all), the flattener in CS4 will put the shadow behind the background rather than in front. In both cases, though, using a RIP and/or viewer which is set to honor overprints will avoid the problem, and allow the artwork to render correctly.
You say that all colors are CMYK. Are you absolutely certain that the background (whatever the rectangular shadow-containing "boxes" knock out) is not a spot color? Your problem description would be more easily explicable if it were.
One workaround suggested was to export the file as a JPG or EPS and save as a Photoshop PDF. We did that on one ad that will run Monday, so we'll see. However, that makes the files with photos enormous -- like from 4 mb to 26 mb
This in itself suggests that these folks do not know what they are doing (though I know that's not terribly helpful to you if you need to advertise with them). I must say that given current economic realities in the newspaper business, it's hard to image a paper refusing to cooperate with a paying advertiser - especially one who has been previously bitten - if not by the newspaper's own incompetence, at least by their unwillingness/inability to provide a proof.