I have the same issue in Affinity Designer. But I don't want to rasterize the vector logo, since it will lose quality in the printing or when resizing it.
I notice that the setting in the CMYK were change by themselves. I wanted a totally black background, but then after exporting the file to PDF, I checked the CMYK setting and they were moved to have a grey.
I have to erase the rectangle background and redo it, then after selecting the rectangle layer, I moved the settings CMYK in Fill to 100% all of them. Nevertheless the Stroke setting were different, and I was not using Stroke, so I moved the to 100% too.
After a few tries changing these setting and exporting to PDF, I finally could keep the setting in totally black.
Thank you,
Bogar
Motor Voter Flyer bk.afdesign