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Purge the disk cache and media cache, either via the "Edit" menu or the preferences. Also turn off multiprocessing (in case you are using it). The issue very much sounds like a problem with concurrent file I/O and a bottleneck situation resulting from it.
Good suggestions. When I rendered as a PNG sequence, that made AE suddenly able to render about 90% of the frames...but the remaining ones still lack the video (or have it rendered in some odd form...like just one field).
Is my only option to go through each of those frames, wait for the comp preview to render, then save the image manually?
Is this just a product of AE not working well with HDV footage?
If this happens to anyone else, I found a workaround. It's slower than crap, but it works for now...until AE can deal with HDV footage better.
Like Mylenium said, trash multi-core rendering, that was an important step. On my quad core machine, I threw about 80% of the RAM to the cache, and had it render WITHOUT OpenGL as a PNG image sequence.
After Effects halted 5 or 6 times during the 4,000 frame render. It would usually have a bizarre error, then Windows would complain about virtual memory. I would just dismiss the error, reload AE, and begin rendering from the last good frame. It took a few hours, but I got all the frames, then rendered the image sequence to a movie.
Tedious and frustrating, but it worked. Hope this helps someone else in the future.
Actually AE is quite good with HDV these days, but of course there are minute variations in the streams depending from which camera it comes and how it was captured. OpenGL is indeed not advisable for final rendering, but depending on what you have done, AE may never have used it to begin with (it will disable it quietly if it encounters a conflict with the render settings and effects used). Still, that checking might be part of the problem as would be the concurrent usage of the graphics card in such cases (as in theory, you would then also have to have 4 of them for 4 multiprocessing instances of AE). In the medium run, if you can't get rid of the issues, I can only recommend to convert the footage before using it, as lame as that sounds.
Did you try to set the "secret" preferences to purge every frame during the render? Perhaps that would have helped too. Either way, glad you got the situation resolved.