Intermittent Bug when saving pdf files in Illustrator CS6

I save a pdf file in Illustrator CS6 with a specific art board size. When I open it in Acrobat the size is off. When our print's RIP's the file, it is off the same amount. I will re-open it in Illustrator and re-save it and just change the name, the artboard is then correct. This is very intermittent. It has happened on two copies of CS6. Both prograns are current with the updates. I am on a iMac running OS 10.6.8.

Document size is: 36.01 x 98.12
I can open up both documents in Illustrator and they are identical.
We have been using these presets for a couple of years without issue. The problem started happening about 3 weeks ago on 2 seperate computers. We have not seen the problem with CS5.5 and earlier.
Below are the preset settings summary:
Warnings
Adobe PDF Preset: CCC High Res PDF 
Compatibility: Acrobat 6 (PDF 1.5) 
Standard: None 
Description 
          [Based on 'CCC High Res PDF'] [Based on 'CCC High Res PDF
          04-28-08'] PDF Workflow For Custom Color Corporation Output
General 
          Preserve Illustrator Editing Capabilities: On 
          Embed Page Thumbnails: On 
          View PDF File after Saving: Off 
          Optimize for Fast Web View: Off 
          Create Acrobat Layers from Top-Level Layers: Off 
Compression 
          Color Bitmap Images: 
                    No Sampling Change 
                    Compression: None 
          Grayscale Bitmap Images: 
                    No Sampling Change 
                    Compression: None 
          Monochrome Bitmap Images: 
                    No Sampling Change 
                    Compression: None 
          Compress Text and Line Art: Off 
Marks and Bleeds 
          Trim Marks: Off 
          Registration Marks: Off 
          Color Bars: Off 
          Page Information: Off 
          Printer Mark Type: Roman 
          Trim Mark Weight: 0.25 pt 
          Offset from Artboard: 0.083 in 
          Use Document Bleed: On 
Output 
          Color: 
                    Color Conversion: No Conversion 
                    Profile Inclusion Policy: Include Tagged Source Profiles 
Advanced 
          Subset embedded fonts below: 100 % 
Security 
          Document Open Password: Off 
          Permissions Password: Off 
          Encryption Level: High (128-bit RC4) - Acrobat 5 and later 
on: Off 
          Printer Mark Type: Roman 
          Trim Mark Weight: 0.25 pt 
          Offset from Artboard: 0.083 in 
          Bleed Left: 0 in 
          Bleed Right: 0 in 
          Bleed Top: 0 in 
          Bleed Bottom: 0 in 
Output 
          Color: 
                    Color Conversion: No Conversion 
                    Profile Inclusion Policy: Include Tagged Source Profiles 
Advanced 
          Subset embedded fonts below: 100 % 
Security 
          Document Open Password: Off 
          Permissions Password: Off 
          Encryption Level: High (128-bit RC4) - Acrobat 5 and later 

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