Thanks James for the tips!
It could indeed be a PTS issue but seems not.. Tweaking some setpts parameters did not fix the pb. Thanks to ffprobe, the time of the first frame is 0.00 and a setpts=PTS-STARTPTS does not have any effect..
The only way I can fix this is to trim the file with the -ss param:
ffmpeg -ss 19:35:31 -i in.webm -vcodec copy -acodec copy -f webm out.webm
only few bytes are then removed, and it's ok. BUT, the only way I can get the *right* start time is to read the file in a HTML5 video player and copy the time value manually. I cannot get the timecode from any shell tool, and then my production system can't guess the value automatically for now.. :(
cheers,
G