FFMPEG File Conversion To FLV

I'm using FFMPEG for the first time. The upload works. The *.avi file is uploaded to the virtual path just fine. When it runs through and attempts the conversion to an FLV file, it doesn't error out - but it doesn't convert the file either. The ffmpeg.exe and pthreadGC2.dllare in the same folder ({virtual_path}uploadvideo). I do see a cmd window flash when the process starts but can make out anything displayed.

Here's my code:
File Upload
Protected Sub Submit1_ServerClick(ByVal sender As Object, ByVal e As System.EventArgs) Handles Submit1.ServerClick
If Not File1.PostedFile Is Nothing And File1.PostedFile.ContentLength > 0 Then
Dim GetFileName As String = File1.PostedFile.FileName
Dim fn As String = System.IO.Path.GetFileName(File1.PostedFile.FileName)
[Code] .....