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You have three options:
1) Use the Encoder 9 you have now, only modify the Pocket PC profile (click the "Modify ..." button to the right of the name), and change the video codec from Windows Media 9 to Windows Media 8.1. You should also double-check your audio setting and make sure it's set appropriately (that is, the bitrate is what you want). It's okay if the audio codec is WM9, it's downlevel compatible.
2) Use the Encoder 7 tool available from Microsoft's Windows Media download page. You'd have to remove Encoder 9 first, or do this work from another machine. Encoder 7 makes fully compatible WMVs for PPC with it's profile.
3) If you are running Windows XP or Windows Millenium, Movie Maker v1.2 has profiles for creating WMV files for the Pocket PC as well. This version is available at Windows Update.

Galan Bridgman
Microsoft MVP - Windows XP Digital Media