As of 25-September-2007, J.River has taken over development of the flac plugins. This site is maintained for reference only.
You can install over previous versions. Download the zip file and extract the contents to a temporary directory. Double-click the *.mjp package file and Media Center will install the dll to the correct directory and register it.
It works for me. May not work for you. No warranty is implied. See the GNU public license.
Previous encoder versions defaulted to Quality = 5. Newer versions default to Quality = 6. You can update your encoder settings in Plugin Manager->Encoders->FLAC Encoder->Settings. There are also now some check boxes to allow you to not add the seektable (defaults to 99 points) and the padding block, though the padding block will get added by the Decoder by default. You can also turn on encoder verify. Please let me know if there are other settings you would like to enable/disable.