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An interactive PDF will always be RGB. Try checking the Transparency Blend Space of the document.
Cheers, but I forgot to mention that it's set to Document RGB.
After hours of trying to figure out how to fix this, I finally did it! Granted, it's a workaround, but still.
It seems that, for some reason, InDesign ignored the Transparency Blending Space option for the pages that actually had transparencies in them (ironic).
So found this fix whereby I set the opacity of one of the transparent elements on each page to 99.9% to force the program to take notice, as it were, and voila! The PDF looks just like it was intended.
Good job and thanks for sharing.
Basically, the Interactive PDF shows some pages with muted colours and I suspect it's some sort of conversion from RGB to CMYK.
When you export to interactive PDF all color gets converted into sRGB, so depending on how you set up the document you could get a variety of color conversions on export. For example if your doc's assigned RGB profile is AdobeRGB and you have CMYK color on a page with transparency the export conversion of the CMYK color would be CMYK>AdobeRGB>sRGB.
If the document is primarily going to be interactive you can make sure all of the color is sRGB and there will be no color shifts on export. Set the assigned profile (Edit>Assign Profiles...) to sRGB, the Transparency Blend Space to RGB, and use RGB colors and swatches.