I'm using flowplayer.pseudostreaming-3.2.7.swf with lighttpd/1.4.28 + h264_streaming module and still such problem exists. Seeking to 00:00(and replaying too) fails and playhead stands on it's place but video starts from begining. But if seeking wasn't used and video played till the end, replaying("Play again") works right. I have noticed that this problem related only to mp4 files. Seeking in flv files works right.
I tested h264 streaming module by checking md5 sum of several downloaded files. Fileshttp://host/file.mp4 andhttp://host/file.mp4?start=0 are equal. So problem isn't in webserver.