Forcing After Effects not to use the Microsoft DV codec
 

Microsoft's DV codec is forcing me to use intermediate files to pass videos between Vegas and After Effects because they render DV files differently. Is there a way to make After Effects use the Sony or Mainconcept DV codec?

You mean when rendering your AE project out? That's a piece of cake. Add your AE timeline to the Render Queue. Next, click the down pointing menu arrow for the "Output Module" (the Output Module should say Lossless by default). Choose "Make New Template...". In the window that opens choose New. You should now have the Output Module Settings window. Make sure the format is Video for Windows, and then choose the Format Options button. Under the Compressor drop-down menu choose the DV codec you want to render out to. Hit OK. You're back to the Output Module Settings. If you want to render audio with your video check the Output Audio box, and set the sample rate. Hit OK. Now give your new Output Module a name in the Settings Name box, and hit OK again.

You now have a new Output Module that you can quickly access in the future in the Render Queue. Just click the Output Module drop-down menu and choose the name of your preset.

Sorry, I mean importing videos captured with Vegas into After Effects.

Uh, well, in that case as far as I know AE has no choice but to use the codec the video was captured/rendered in. How else could AE process it, without rendering to another codec/format?

If you're having problems, my advice would be to render out of Vegas using a different DV codec.

By the way, doesn't Vegas install and use a different DV codec than the Microsoft codec?

Unfortunately, that is not the case, because some codecs are interchangable in the sense that they work, but they do not have the same results. DV is a good example. I captured with Vegas, but After Effects does not use Sony's DV codec when importing the footage. This means that anything I do in After Effects sticks out when I bring it back into Vegas unless I use a codec they can both agree on (I use uncompressed for now).

Whoohoo! I think I found a solution for you. After Effects has a file named interpretation rules.txt (in the program folder's Support Files folder) in which you can specify import rules for footage, including the codec. Look up "interpretation rules" in the HTML help file and it will explain everything you need to know to edit the file.