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I have an Illustrator file with a placed PS file as the background with other vector element that use transparency. This PS file is CMYK with an extra spot colour channel. There is only image data in the black channel and the spot channel, nothing is in the CMY channels. The black channel has a random texture, the spot channel, PMS 728 is solid, the intent is to simulate brown paper. The rest of the Illustrator file is black text and vector art in a second spot colour....pretty straight forward in my view.
I save out of illustrator as the latest PDFx version. When viewed with separations in Acrobat it shows all separations as they should be. Black and 2 spot colours.
I then bring this file into AGFA Apogee 11 with the intent to output printing plates. The problem is when it renders it converts the black separation into a 4 colour black. Instead of hving 3 plate separations I now have 6...the black, which converts is now a 4 colur black. I suspect it has something to do with transparency but am not sure. Is the version of PDFx I a saving to the wrong one?
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If it appears correct in Acrobat you probably need to talk to Agfa support. However, one precaution you can take is to be sure that the CMYK profile you assign is the same one that the Apogee workflow uses. Otherwise you can expect (you are demanding) CMYK to CMYK conversions that will run to all plates.
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A 5C Photoshop file can be problematic, you could try saving it as a Duotone (K+Spot) or remove the spot color and save as a grayscale, adding the solid spot color in Illustrator, save as the Illustrator default PDF.