@AdamTheBoy: not yet. Dirty trick: you can try to process the video with a tool that doesn't know about dual ISO, then drag the DNG files over cr2hdr. This may not work with the latest one, because it relies on the black bars (not present in raw video files), but with the older one (or cr2hdr_exp, look it up in the thread) should work just fine.
@ted: it reads one line, skips 2, and I don't know how to change it. I think it can be shifted somehow with ADTG registers, but this area is still a mistery.
To hide color aliasing where I can't recover it, I do some median filtering, but I believe all serious converters do it (dcraw does, I took the algorithm from there).
@tron: solved, download again.