Where are you viewing the PDF? In AcrobatPro XI the two PDFs appear to be identical both in resolution and color.
The color is all device CMYK (no profiles), so the preview of the CMYK color will depend on the reader application's color management capabilities or settings. Try exporting using either PDF/X-4 or PDF/X-1a if you want to force everything to CMYK.
We are viewing the pdf in acrobat pro XI.
When I look at the two files, the cs5 version is blurry compared to the cs6 - color is the same.
When I look at the file open in InDesign, it is darker and richer than the cs5 or cs6.
Are the application color management capabilities or settings different from Acrobat Pro XI and InDesign CS5 or CS6?
The X-1a exporting from CS5 looks much better than the normal output, and better than the CS6 output. What would cause that? I want to understand this, as it opens up a world I did not know existed.
I'm not seeing any color differences here, either. I'm on Acrobat 9.
Are your color settings the same in both versions of ID? Are you using the same simulation profile when using output preview for both files in Acrobat?
The X-1a exporting from CS5 looks much better than the normal output, and better than the CS6 output. What would cause that?
If you export a CMYK PDF with no profiles and open it in AcrobatPro, Acrobat's Color Management's Working CMYK space handles the preview. So here's the difference between two very different profiles Fogra Coated and SNAP Newsprint:
When you export PDF/X-1a an output intent profile is included (usually your document's CMYK profile) and that is used in Acrobat for previewing CMYK instead of the current CMYK working space.