CS4 Rendered output playback differenent from timeline monitor

I have an interesting problem here. I have about 20 clips which have been trimmed in the source monitor, by setting in and out points, and then dragged to the timeline. When scrub or hit enter to render the timeline, it looks great - exactly as I expect. However when I export it's as though the in and out point of each clips are being ignored and it looks totally different.
I have a feeling I'm missing something silly - has anybody seen this before?

The clips i'm using are 1080i 60fps
I'm outputting to H.264, scaling down to 720
I'm using a quad core laptop with a NVIDIA Quadro FX3700M graphics card.
I recently installed a trial verion of Nvidia Elemental Accelerator. This hooks into PP and comes up as a set of different output options during render setup - i.e ELEMENTAL.H.264 as opposed to H.264 - selecting the elemental option seems to be causing the issue When I switch back to the reguar output settings no issues. I'll post this to the NVIDIA board as well.
One other thing - I did check the NVIDIA website and found I didn't have the up to date driver (duh!) - that's probably all the issue was.
Thanks again for your responses!

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