Problems updating itunes and quicktime
It not just transcode your MP4/MPEG files into proper formats which i Tunes can compatible with, also can edit your raw files before loading.
Though i Tunes have claimed that they can support MP4, MPEG-4, WAV, AAC and Apple Lossless.
But unknown transfer problem will happen during the progress.
(Learn more about the supported formats by i Tunes). Your MP4/MPEG files have already existed in i Tunes, but you cannot find them Starting from i Tunes 11, all the movies aren't purchased from i Tunes will be added to "Home Videos" under "Movie" Category.
You can change the category that your MP4 files shows in i Tunes so that they will appear correctly in it.