fwiw, I've mistakenly used place dialog set to crop for ages, it's a hard habit to get into trim, but I have yet to see a difference between crop & trim.
Can anybody elaborate on the subtleties? Perhaps the OP has place to crop as an option?
And, my 10.4.1 struggles to run CS3, I'd hate to try to get CS4 running in a production environment.
I very faintly remember someone having this exact problem a while ago too. Of course there is the other feature (bug) in CS4 in earlier versions that resulted in problems when you were using the bounding box to crop PDFs, it shouldn't relate to this one but it might be worth looking into. The readme file for one of the later dot releases should detail it. As a work around does setting the crop box the same as the trim fix it?
On another side note I recently discovered this way of setting the place options, you could try that to see if it makes adifference but I doubt it would.
@ Daniel Flavin, the difference between the crop and trim is exactly that, the trim is the page size you've set in an Indesign document that you've exported to PDF, while the crop is the overall size includign bleed and slug (if any) if you've included them when you exported the PDF.