Question.

When I try to convert an AVI file, I get a file with no output (other than the Pocket DVD trailer.)

Answer.

Usually this is a codec issue, especially on avi files encoded using the DivX codec.
 
If you try uninstalling all DivX, Xvid or other Mpeg4 codecs, and then just re-install one, such as the main codec from http://www.divx.com/ 
this usually sorts the conflict, and allows you to convert sucessfully.