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Sounds like a flattening issue with spot colors.
What are your export settings?
I don't know what I initially used to get it to render with the transparency, I think that is the key.
Using Export > Adobe PDF (Interactive) > ...
Here's my question, the ... area has a Image Handling, Compression piece to Automatic, but after reading the next field it seems it's converting the images to JPGs which means they will not have transparency. Which Export feature should I be using?
What in the world, whatever I did that time it worked. I guess the key was to set it to Interactive with the Compression to Automatic? I could've sworn I did that already multiple times.
Ah, it may have been the checkbox, "Create Acrobat Layers".