Tivo Desktop does not recognize many the file extensions such as .mkv, and such, only a few like .tivo, .mpg,, to name a few.
Tivo Desktop Plus will recognize a few more but that's $25.
PyTivo recognizes a lot more files and has more features, and its free.
Original S1 (Recycle Heaven)
Series 2 (PLS, sold)
TiVo HD 1TB (157 HD Hrs, PLS, "652")
Juliet Basic (4XL, PLS)
The TiVo Apocalypse begins on Sat 2013 Feb 16 00:00 GMT!