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I also had no luck using Vuze to transcode MKV (Matroska) files for my Tivo HD - in my case the video would come through but the audio would just be a continuous screech.

I now use pyTivo for transferring between my PC and Tivo HD. And also, PyTivo transcodes on-the-fly, so a file doesn't take up double space on the computer like with Vuze, which makes saves it's own transcoded copy.

I have solved this problem by cribbing from the "Generic DirecTV" profile, which creates working VOB from MKV.

Found in directory:
C:\Documents and Settings\<Your username here>\Application Data\Azureus\plugins\vuzexcode\profiles

File is called:
TiVo_HD.properties

Modify the contents to match this:
#General information
name=TiVo HD
device=tivo.series3
file-extension=.vob
icon_url=http://cache2.vuze.com/devices/tv-hd.png
description=

#video information
video-max-width=1280
video-max-height=720
video-pixel-mod=8;
video-max-frame-rate=30.0

video-args= -vcodec mpeg2video -b 20000k -maxrate 35000k -bufsize 4096k
#-f vob

#audio information
audio-allowed-bitrates=32000,48000,56000,64000,80000,96000,112000,128000,160000,192000,224000
audio-allowed-sample-rates=32000,44100,48000
audio-max-channels=2

audio-max-bitrate=448k
#audio-allowed-bitrates=448k
#audio-max-sample-rate=48000
#audio-max-channels=2
audio-args=-acodec ac3

#container information
container-format=vob

I'm not sure what fixed it. I commented out the -f property in the command line and added more acceptable bitrates to the bitrate list. The Directv also had the MaxChannels parm set, while tivo had it commented out.

Works great!