Help - Getting slower render times with AE CS6

Hi everyone
Wonder if anyone else is getting as described?
I have a 3m37s project which is predomnantly motion graphics using live shot footage (.MXF files), Illustrator and a few JPGs.
In CS5 AE I get render times which average around 45mins, so I thought I'd see how quickly CS6 could crank it out by - as you can see I'm getting times which are in excess of 2 almost 3hours!
The project contains a few 2.5D moves as well as tiny bit of Trapcode 3D Stroke
I have mentioned on this forum that I'm having the Error 5070 problems with start up and Ray Trace is unavailable but these times seem seriously wrong to me.
Mac Pro 3,1 (2x 2.8GHZ)
20GB RAM
OS 10.7.4
NVIDIA GeForce GT8800
NVIDIA Quadro 4000 both on GPU Driver 207.00.00.f06
CUDA Driver 4.2.10
All files are on a 2TB drive (7200rpm)
Rendering to a 1TB drive (7200rpm)
Corsair SSD 60gb Cache drive
As an observation when I watch the frames counter ticking over, CS5 seems to steadily work it's way through the render at around less than a frame a second, CS6 seems to crank out 2-6 frames then hold for 30secs before working on another batch. It crawls to a halt near the end.
Can anyone offer any help or advice?
So far I'm not having a great time with my CS6 transition
Thanks
Rob
Message was edited by: Bokeh Creative Ltd
because of a Typo

Thanks Rick - Yes what confused me was that it only took 45mins in CS5 even with MP 'on'
Still having no joy with Ray Tracing though, even though I have a Quadro 4000 card, I get the 5070 error on start up. Any ideas?

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