I teach 3D animation using a Windows lab. I need to export out of AE and allow the Video teacher to take it into Final Cut. When I export a DV stream or QT, I get much worse quality than MS DV avi. My video teacher said to use the QT DVCPro codec, but the video is much worse quality than avi. I have had similar problems going from Windows Premiere Pro to Final Cut.
Anything to do with DV in QT is more or less busted on Windows (Apple's fault). If you wanted to use it, you would require a third-party DV CoDec from Canopus or Blackmagic or whatever. Using Animation or PNG is much more advisable. If you don't need Alpha channels, even Photo-JPEG at 75% quality will do (looks almost identical to DV in terms of artifact distribution and has reasonably small file sizes). For long-term archival or for quality productions like students' end-of-year projects, you may simply consider investing in a lossless commercial CoDec (Microcosm, Cineform) or a number of external harrdrives and render to image sequences (OpenEXR, PNG, TIFF).