To answer my own question...

The problem is with mencoder using both stdout and stderr for output.  CF only 
listens on one, so mencoder can't send some of its output anywhere, and hangs.

The solution it to redirect the stderr output to stdout.

This is my line from the batch file:
mencoder "%1" -o "%2" -of lavf -oac mp3lame -lameopts br=32 -af 
lavcresample=22050 -srate 22050 -ovc lavc -lavcopts 
vcodec=flv:vbitrate=340:autoaspect:mbd=2:trell:v4mv -vf scale=%3:%4 -lavfopts 
i_certify_that_my_video_stream_does_not_use_b_frames > convertmov2flvoutput.txt 
2>&1

Notice the 2>&1 at the end?  That's the puppy...  Pipe outout2 (stderr) to 
output1 (stdout).

Hope this helps someone...

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