Hello,
I have encountered the same problem. Attached I send the file color.afpub (the file has been simplified to such an extent that it only contains the actual problem).
On the bottom of the page are two horizontal rectangles, both 30mm high and overlapping each other for 2mm. Thus, it looks as if there is only one rectangle, but there are two. The upper one is the result of a cropped image and the lower one is a rectangle object that has been created in Publisher.
They are not absolutely black, but almost. The lower rectangle gets the color assigned from the upper rectangle. When checking the color values with the color picker tool, both rectangles show the same CMYK-values.
However, after this page has been exported as a PDF, the two rectangles have different CMYK color values.
This can be easily duplicated when exporting a PDF from this file, opening the exported PDF in Publisher and check the color values with the color picker tool. If I use another PDF editor, I can also detect that the colors are not the same anymore when exported as a PDF.
How is it possible, that the colors change when exported as a PDF? I use Affinity Publisher 1.10.4 on Windows 8.1.
Color.afpub