Question about overwriting PDFs

I'm having a problem overwriting PDFs from InDesign or Illustrator.
This isn't the same issue people are having where they're prompted that the file cannot be overwritten. I can save over the file no problem. The issue is when I open it, the old version comes up. Funny enough, the thumbnail preview in Finder actually shows the correct version, but the file itself is incorrect.
I've tried deleting the PDF and saving a new version. Because of my workflow, I have to keep all versions that are sent out named and numbered properly in sequence. So when I name it the same way the old one was named, the old version still shows up!
I'm really not sure if this is an Adobe Acrobat problem, a Creative Suite problem, or an Apple problem.
Just some info on what I am using if it helps: Adobe Creative Suite 6 on an iMac with OS X 10.9.2.
Any insight is greatly appreciated. Thank you.

Sounds more like a systemic problem with your file system and the resource forks are not updated. You should check your volumes with Disk Utility or use tools like OnyX to check for system problems.
Mylenium

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