For those using a HD-PVR with SageTV that want to re-encode to the Ipod, or other format, check out the latest version of Handbrake. They added all the ffmpeg libraries to Handbrake and this means that is can read virtually any file type now. I've been using Handbrake over the last few days to convert the HD-PVR files into the IPod format and it's working really well.
For those interested you can use the GUI. Or, if you want to integrate it into an applicaiton like Dtb you can use the command line version. Below is the command line I'm using.
"C:\Program Files\Handbrake\HandBrakeCLI.exe" -i {inputfilename} -t 1 -c 1 -o {outputfilename} -f m4v -X 720 --crop 0:0:0:0 --decomb -P -e x264 -q 0.39 -a 1 -E faac,ac3 -B 128 -R 48,0 -6 stereo -D 2 -x level=30:cabac=0:ref=3:mixed-refs=1:analyse=all:me=umh:no-fast-pskip=1 -v
A really easy way to comeup with your command line is to enter the Handbrake GUI and use it to configure all your settings. Then tell Handbrake that you want to add your show to the Queue. Then from the queue manager you can select an option to export the queue to a batch file. Inside the batch file you will see the command line option for your show.
This is an interesting open source alternative to DirectShow for those that have issues getting Directshow working.