Large H.264 files causing freeze when placed on Timeline

This is in reference to Encore CS5.1 that came in my CS5.5 production suite.
I have BD project that I am using x264 output files for. I have three timelines. One is 1 minute long (some credits), another is about 5.5 minutes long and the main timeline is about 94 minutes long. I use the same settings for all three .264 files. When I open and import the files into Encore it takes notable time to index the files, but does read them all in. I can play each .264 file in the preview window above the asset tray. I have timelines working and playing for the 1 minute piece and also the 5.5 minute piece. When I create a timeline for the long piece, I place my AC3 file on it, no problem. When I try to place the large .264 asset into it, I get a cycle of CPU and RAM usage that seems to run about 20-30 seconds with one thread of the CPU very active and the RAM usage climbs about 1.5GB. So, I am not sure how to finish this project up. I have been at it for a few days trying to get this to place into a timeline.
Details:
     Machine : Win7 with all updates, i& 3960X Hexacore (12-thread capable), 64GB RAM, Video workspace drive 8TB RAID10 G-Speed esPro via ATTO R680 miniSAS raid controller. Matrox MX02 LE external via PCIe card (not really used in this contect) Machine is dedicated to video/audio work. Primarily have Adobe CS5.5 Creative - Production Premium on it. I also have TMPGENc Video Mastering Works 5.
File details: Using THMGENc VMW5, I have access to CUDA supported encoding as VBR 1-pass, or they implement the x264 engine with BluRay certified wrapper settings. I have tried using VBR 1-pass output via CUDA encode, x264 output set as 2-pass VBR and also CBR.   The encode rate is set to 23000 with a max at 29500 for the VBR modes. The files are coming about about 16.5GB-17GB.   The GOP is set to 30, and I have tried both open and closed GOP.   The material is 1080i 29.97fps NTSC.
I could try the Mainconcept based AME compression, but I have never wanted to wait THAT long. The x264 runs about 4 hours on my machine, and the CUDA based compression runs about 30 minutes (faster than my Matrox MXO2 !!).
I have used this same setup (both VBR 1-pass with CUDA and also VBR 2-pass with x264) on numerous projects, but they all seem to be no larger than about 30 minutes per piece.
This long piece is a graduation ceremony and there really isn't a very good place to cut the timeline into sections. I would prefer to figure out what the problem is and fix it rather than dance around it.
Is this a known issue with Encore CS5.1? Is there any workaround or changes I can make to get this done in one piece?   Or should I just give in and make it multiple 30 minute pieces?

I found a work around that I am surprised worked. In place of my normally used pre-encoded H.264 file, I imported the 850GB 10-bit AVI file and used that on the timeline with the pre-encoded AC3 file. It was much snappier and I was able to place proper chapter marks as such. When I was ready to build the output folder, I selected the AVI asset and right clicked to "Locate Transcoded File". I selected my original 2-pass VBR x264 derived file that I had been trying to import and use. Encore went off and looked the .264 file over and came back as happy. So, I built the output folder and it did not attempt to transcode anything and the resulting BluRay works just fine on my standalone player.
I really think this is not a "solution", but rather a work around. What seemed to be happening in the process viewer was Encore (obviously a 32-bit application) was settled with a memory charge at about 1GB. As it was doing it's thing, about every 20-seconds, for about 20-seconds, the memory charge would climb from 1GB up to about 3.1GB or 3.2GB and then the NT Kernel would pop up as active and then the memory charge for Encore would be back to 1GB again and no CPU activity for a 20-second cycle. It would just keep doing this. I watched this happen for a few hours before killing it. The CPU loading each time it was active was a full 1-threads worth. So, perhaps there is something in my Win7 x64 environment causing a problem, but I have tons of RAM and hard drive space and my processor is no slouch.
Just why Encore was happier with the massive uncompressed file than the compressed on is beyond me. I mean, placing 850GB on the timeline took just a handful of seconds.

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