AE CS6 renders 7-68 frames out of 889, but gives the "ding" and claims it's done!

Question

So, I set up my first render with CS6. Nothing too complicated, 889 frames long. I hit "Render" and it starts.
About 30 seconds later, I hear the "ding," and am surprised to see that according to the program, the render has finished successfully. "Wow," I think, "CS6 sure is fast. A little *too* fast..."
And sure enough, the render only exported 13 frames! Umm, odd. I check my settings and yes, I've set it to export the entire comp (the Work Area spans the entire comp anyway).
Okay, strange fluke. Try again.
7 frames. "Ding!"
Ugh, try again...
15 frames. "Ding!"
And so on... 68 frames. 35 frames. 9 frames. 37 frames.
What the hell, man! Why does AE think it's done the render successfully, instead of throwing an error? This is completely unacceptable. Obviously I'm not doing anything wrong here, otherwise the number of frames would be consistant.
When I import the partial renders back into the comp, lay them on top, and export again (to avoid re-rendering those frames), I can get a longer export. So clearly the problem ony comes when there's real work to be done by the renderer, but it never renders more than 70 unique frames each time, and usually I get far fewer, 15 on average.
This is just stupid, I can't live like this. There's no logic to this problem, which pissed me off so much that I punched a door.
I've had nothing put headaches with AE CS6 (the new 3D renderer won't initialize with my CUDA GPU, and refuses to fallback to CPU; Dynamic Linking is slower than CS4, etc.), but I've been able to put off troubleshooting these problems so far, and I wasn't worried because there's always an answer out there somewhere, but this is a frickin' showstopper.
Please help!

Answer 1

I'm using the default "Lossless" (AVI) settings in the output module, sometimes "Lossless with Alpha" or similar setting. I almost exclusively use uncopressed renders for all my AE projects, as I prefer to use AME or PrPro when rendering out to compressed codecs.
I've been working with multiprocessing disabled for awhile, so I haven't had to deal with this problem. But I have a moment to breathe between jobs now so I can more fully describe my setup, and run some tests.
Most (but not all) of my projects have been largely made up of RED footage (r3d files from the original RED ONE as well as Scarlet/Epic), both 1080p and 4K. But I also frequently work with DSLR footage in the dreaded h.264 format (both mpg and mov). Performance within the program itself (including previews) seems quite good, regardless of which codec my layers are made up of.
For effects and such: some projects have nothing but text layers and masks, while others have extensive keying, color correction, and animation. And some use the 3D ray-tracer and are made up of nothing but shape layers and color mattes, having no video footage at all.
Since I last moaned about this issue, I have re-installed the CUDA toolkit (instead of just the graphics driver), and now the ray-tracer is working better, and Dynamic Link performance is better, but unfortunately, the problem described in the original post remains...
When I have Multiprocessing enabled, any render of a comp with more than one layer seems to exhibit this problem. After trashing my preferences, I have been able get a succesful render or two with multiprocessing enabled, if the project is not too complex, but soon after the problem returns for all projects (it's hard to be precise about exactly when, and what project, triggers its return). I have no idea if trashing my prefs has anything to do with granting a momentary fix, or if it's just a coincidence. When multiprocessing is disabled, I generally have no problems of any kind when rendering (other than it being much slower, as expected).
My system:
OS: Win7 x64 SP1
CPU: Xeon E5504 (x2) @ 2.0 Ghz (8 logical cores total)
GPU: Quadro FX 3800
RAM: 24 GB
Multiprocessing settings:
RAM for other programs: 6GB
RAM per process/core: 2GB
Processors reserved for other programs: 0
Actual background processors used: 7 (this drops when I have PrPro or AME open reserving its own RAM, obviously)
NVIDIA driver: 301.32
CUDA version: 4.2
I can't seem to identify anything unusual about my setup or configuration, and my Multiprocessing settings use recommended guidelines from the AE team (which have proved optimal in the past).
Is there any other information about my setup that would be useful?