I've copied my full rez Sony HDV files to Compact Flash and they play back flawlessly.
Detonate, how are you extracting your files and are you just keeping them as raw M2T or encooding them at all? How has Roku been for performance on playback of these files. Sounds like CF works great but not so well on off a share? What are you using to store your video (NAS, etc..)
I own the Sony HC1 and am trying to find a decent solution for storage and playback. I prefer to not encode the videos since storage is relatively inexpensive in the long run.