What codec are you rendering to? Perhaps render to another format, and then see if you could rerender that for your avi. If you have premiere or another compression program, you could load your rendered image sequence (or lossless QT:Animation) and compress in that.
And "advanced editing" and "After Effects" are a bit oxymoronic.
Well to be honest, I'm not very familiar with rendering in after effects. All I used to and still do is just, when I'm done, click export right away.
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Rather than use "Export", use the more advanced Render Queue:
When your composition is ready to render, choose Composition/Make Movie. Choose your Render and Output settings, then hit the Render button.
If you explain what your output target is (Web, DVD etc) we can suggest more specific details.
Read more about the Render Queue in the AE CS4 Help files.
Ah - that's your problem.. Don't use File/Export. Instead use the Render Queue (read up in help for more info than I can type...)
To render your movie, set your work area for the full amount you want to render. Hit ctrl-m to Make Movie (adds it to the render queue). Set your options and you should be good to go. Realize that AE can't do multipass compression, so as I mentioned before, you might be better off rendering to a lossless format (tga sequence with RLE enabled, QT:Anim) and then compressing it in another program.
Also, some formats require specific resolutions.. If you are still having problems, please mention your comp settings, render settings, and render format/codec.