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Do you have layers accidentally set as Guide Layers? Those will show in Ram Preview, but won't render.
The layers that have the transition on them show up in my final render - up until the frames where the transition occurs...so I don't think that's the problem...although I have also double checked this - and they are not set to guide layers.
If I turn off Interlace when I export my comp, the transition effect works in either TGA Sequence or DV AVI...
Maybe there's something I don't know about Interlacing & Rendering from After Effects...any suggestions out there?
I can repro this. The source footage has to be interlaced and you have to render to interlaced. I played around a little- it doesn't occur if you reorder the effects. It seems to have something to do with the animated Opacity control on the Solid Composite effect in the preset. I can also make it happen with completely different effects (Bulge and Fractal Noise), as long as the second effect has an Opacity control that is animated.
I filed a bug with Adobe about it.