Justin,
What happens if you set the profile for printing to GRACol to match the CMYK in your document?
The irony here is that we very often get complaints that printing from InDesign yields the wrong colors and that printing from PDF via Acrobat or submitting the PDF file to a direct PDF RIP solves the problem.
One additional recommendation.
Why don't you try exporting your PDF from InDesign using the PDF/X-4 joboptions? That just might solve your problems completely. Try that and let me know whether that works! PDF/X-4 is what we most strongly recommend for reliable color and reliable PDF print publishing workflows.
- Dov