I have had so many issues like that and I found a way solve them all by setting the RENDERING INTENT in the Default color management settings to PERCEPTION instead of Relative Colorimetric. Also, once that change applied, be sure to create your PDF file with the same ouput colors as your original file objects... RGB to RGB and CMYK to CMYK...Personally, I only use the NATIVE output when I use spot colors like PANTONE or others. I don't know if that might be 'professionnal' solution but I've never had issues since.
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