I haven't tested a fresh SVN build in a while, so possibly some other things have broken along the way. Will do a new build shortly and see what I get.
I really haven't looked enough at the MP4 format spec to know what needs to go into the moov atom. I assumed it was a frame index, and if that's the case then you obviously can't generate it on the fly because you don't know what the frames are yet. If it's something simpler, it may be possible but I just haven't looked yet.
By the way, it's quite a common problem and there are tons of emails about it all over. This thread, for example