exporting with a transparancy!?

Also, check if the Swatches Color Type is set to Spot. A Process color that uses all 4 CMYK inks like yours wouldn’t be affected by the Overprint Fill attribute. Here the top color is Spot, bottom is Process:

Screen Shot.png

Looks like overprint, not transparency.

Check your indesign file in Overprint Preview mode - that will show the transparency in InDesign. Go to View>Overprint Preview

And then open  your Effects panel - my guess is it's set to Multiply.

And if it's grouped it might not show any effects or transparency, if you ungroup it and select them individually - in short groups can have effects separate to individual parts of groups - not sure if that's the case here it's just FYI.