Is the logo a spot color? If you have to export to interactive try converting the spot color to process. If you don't need interactive try exporting as PDF/X-4.

The logo has a green gradient so I guess that means it's not a spot color logo?

A gradient can be made with a spot color. Spot colors have a spot color icon in the Swatches panel. You should be able to double-click the swatch and change it to process:

I want this pdf to be suited for the web so then I should use the INteractive export, right?

Are there interactive elements like buttons? If not PDF/X-4 should keep color unchanged.

To export compliant RGB PDF documents, you need to "Print..." to the Adobe PDF printer profile.  The Export... will not get compliant documents, but going via the print driver will.  I am on Windows, and noticed the color shifts in Reader as well, did some exploring and by using the Print to PDF I get RGB PDF files that do not shift color.

I've been having the same issue.  If I print to PDF the issue does not occur, but I needed to Export as a PDF because the interactive doc format maintains hyperlinks.  After much frustration I've found that the issue is linked to having any semi-transparent element on a page. 

Each of the images are different pages from the same document. As you can see if there is a PNG with transparency, or a JPEG with a transparency applied in InDesign, the colors appear as CMYK "For Print" rather than the expected RGB.

Note that this document was setup for web (Document Setup > Intent > Web).

Unless there are some settings that I'm missing this sure seems like a bug Adobe should fix.

Thank you both for the quick reply.

Rob: I'm using Acrobat X to view.  It seems that if CMYK simulation profile was set then all of the pages would render the same .  The only variable on these images was the transparency but they render differently in the same document.  Your test appears to be using a solid block of color with the transparency set to ~50%. I just check and yes, that form of transparency works fine.  Please try again using a PNG 24 with transparency or by using the Gradient Feather Tool on an imported image.  BTW, the transparency blend space is set to Document RGB.

Peter:  If there are settings that are affecting this outcome that I'm not aware of then I can't really tell you what those settings are. Please let me know which settings I should report back on.

Blend space is RGB:

I am not using a PDF preset for export.  I'm selecting "Export...", selecting "Adobe PDF (Interactive)" from the "Save as" menu...

And then exporting with the default settings in the dialog:

Rob, thank you, this was very helpful.  The document appeared correctly in Acrobat Reader so the issue seemed to be with Acrobat Pro.   The first suggestion didn't seem to help.  Switching the simulation profile momentarily changes the look of the document, but upon closing the Output Preview dialog the colors switch back.

However, the second suggestion worked.  Changing the Transparency Blend Space, applying it to the entire document, and then saving it appears to permanently change the doc - even when closing and re-opening in Acrobat Pro.   It solves the problem, but only for that particular document.  As a test, I exported another version of the same file from InDesign and I ran into the same issue.  Even though the problem appears in Acrobat Pro it still seems like this is a problem with the ouput from InDesign. 

Will I need to change the Transparency Blend Space for every document I output from InDesign inside Acrobat Pro or is there some setting in InDesign that will solve this issue?

As a test, I exported another version of the same file from InDesign and I ran into the same issue.  Even though the problem appears in Acrobat Pro it still seems like this is a problem with the ouput from InDesign.

Have you tried a new document where you choose Web as the Intent from the New Document dialog?

BTW, I did choose Web as the Intent from the New Document dialog for the four test images posted above.  That didn't change the outcome.

This has been frustrating me all day! Working on a client document in InDesign RGB and Acrobat keeps rendering incorrect colour space.

Is there any way to remove this as a default once you export as Interactive PDF? It seems rather painful to have to change the Transparency Blend Space manually for each document.