I think what's happening here is that you're 25P footage updates half as often as your 50P. It's half the framerate, so that's why it's stuttering.
If you can't render the 3D sequence out again at 50P, and you really need your final comp to be 50P, then you're going to have to get After Effects to make up those intermediate frames.
Here's one way to do it:
i) Use Time > Time Stretch on your TGA sequence layer, and set it to 50%. This will make your 25P footage play back at twice the speed. But if you step through, it's only playing each frame once. This is good.
ii) Precomp the layer.
iii) Use Time Warp, Twixtor or your favourite time remapping plugin that uses pixel motion, to stretch the layer back out. If using time warp, set your Speed to 50%.
This will stretch the layer back out again, and the timewarp plugin will fill in the missing frames. Note that this is no way as good as rendering back out your 3D at 50fps. It will get you out of a jam.
Hope that helps,
Ben
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