Just noticed that the Boxee beta update from April 19th now includes manual media correction and addition. This will allow you to fix things Boxee has mis-identified as well as add things Boxee couldn't or wouldn't identify at all on its own.

I haven't tried the new version myself yet, but hope to give it a shot in the next few days. I don't use it full-time either since I don't have a silent nor low-power machine I can leave it running on. All testing is being done on my primary MacBook Pro in anticipation of what will be available in the stand-alone Boxee Box.