Sorry I didn't read your complete problem.
I'm not downloading to a phone, just streaming to local laptops.
I was also trying to find way of using ffmpeg on laptop to do
fast transcoding and then uploading transcoded video to pogoplug for
instant viewing and the above ffmpeg command works fine for me.
For your phone have you tried to resize your video using the size option?
As in -s wxh, where w is the width of your screen in pixels and
h is the height in pixels.
So for 800x600 the ffmpeg command would then be

ffmpeg -i inputfile.ts -b 9000K -ar 44100 -s 800x600 outputfile.flv

ooops: maybe also lower the bit rate to something more reasonable for a phone app.