Media Encoder stalls when using a 2-pass BlueRay H.264

Hello,
This has happened twice, I send the PP timeline to Media Encoder, select a 2-pass encoding, BluRay H.264, and the encoding process starts and runs fine. Three quarters of the way through a 3 hour squence, encoder stops encoding / stalls, and the timer for how long it has left to go, now starts to add time. Before the 'stall', my CPU was working hard, all 8 cores, when Media Encoder stalls, the CPU workload is nil.
If I take the exact same PP squence and setup just a 1-pass encoding using the H.264 Blue Ray codec, all is well, Media Encoder completes the job.
Any idea why the 2-pass encoding doesn't work? I am using CS6 with all updates installed.

I know there WAS a bug http://forums.adobe.com/thread/944584 so it may be that bug was not 100% fixed in CS6

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System Manufacturer
MSI
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MS-7821
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Some general questions/ideas...
More information needed for someone to help... please click below and provide the requested information
-PPro Information FAQ http://forums.adobe.com/message/4200840
What is your exact brand/model graphics adapter (ATI or nVidia or ???)
What is your exact graphics adapter driver version?
Have you gone to the vendor web site to check for a newer driver?
For Windows, do NOT rely on Windows Update to have current driver information
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ATI Driver Autodetect http://support.amd.com/en-us/download/auto-detect-tool
nVidia Driver Downloads http://www.nvidia.com/Download/index.aspx?lang=en-us
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http://forums.adobe.com/thread/592070?tstart=30 for screen shot instructions
Free programs to find file information for PC/Mac
Have you tried the NEW ITEM process to insure your sequence matches your video?
See a link on page #5 at http://forums.adobe.com/message/2276578
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Read Bill Hunt on BSOD shutdowns http://forums.adobe.com/thread/772169
-win32k.sys BSOD http://forums.adobe.com/thread/1404938?tstart=0
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Sally Powell wrote:
When I transcode directly through Media Encoder, the process works fine, but if I ingest using Prelude (where students choose which files to transcode, set destination, etc) the transcoding fails and we get an AME error.
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Howdy..
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