The files are being generated by a Deck Link Pro card that is in an HP server.
.DV files ARE encoded with the dv codec it is just a raw stream that supports 2 embedded audio tracks. QT .mov files are just a wrapper that can contain different codecs (essence) in our case that essence is a DV stream with separate audio neatly wrapped or packaged in a .mov.
Problem is that FCP does not appear to work well with a .dv stream when audio is added to it.