LR's library is crippled by it's fussiness about what files it acknowledges. You've just discovered one of the issues. I never use the LR downloader simply as it may miss video files shot by say my pocket camera. After nearly formatting a card with uncopied videos before realizing this gotcha, I stopped using LR in case I forget that not all files on cards are acceptable to LR.
I'm hoping that the 5DII and the D90 will help Adobe to realize how crippled LR is for photographers, the very people it is aimed at.
This stupidity about file formats has wider implications which basically means you cannot use LR as a DAM app, as a DAM app has to see all your relevent assets to be worthwhile and many of my still images are not allowed by LR [Duh!], let alone other files relevent to my photography, like text notes with names and location info, video footage of possible locations, audio for slideshows.
Whether LR can work on the files is irrelevent as they can simply be handed off to an external editor, just like PS is used for images at present. Though being able to view, label, rank, keyword etc is essential.
