The correct answer here (modifying my original post) would be:
For HDHR you should be using either the HDHomeRun H.264 or HDHomeRun Unprocessed profile and it will work fine. HDHR only supports mpg files for metadata.
Make sure you have enabled the Add Information check box in the expert settings page of the conversion task to add the metadata back to the file after processing.
@techpro2004 keep me honest here 