I can only speak to the Photoshop part. Photoshop is likely doing it when you either flatten it or save/export it. Photoshop doesn't quite have the depth of options for creating PDFs that Illustrator or InDesign do, but if you're not careful it's very easy to compress things and that can rearrange those tiny pixels enough that you're no longer dealing with a 1 to 1 process.
I suspect just flattening it is squirting your pixels around ever so slightly (guaranteed if you're flattening vector stuff), but saving a copy of a jpeg can definitely do this too—Which is what Photoshop will do if you have jpeg compression turned on in the compression tab in the 'save as PDF' window. Try selecting 'none' and see if that has any effect. You could also try saving it as a tiff, which is lossless.
Depending on your image you could also use Photoshop to contract a selection and then nip away a few pixels, making your white plate just a tiny bit smaller than what's printing on top. Not sure that's doable in Rasterlink, but it would be something I'd explore.