I did some investigation on how the web frontend handles new videos.
When uploading a 6MB test video (using the web interface) I get the “premiere video” option as intended.
It seems like the API called is the same I use: a POST request to https://api.twitch.tv/kraken/videos containing JSON-encoded video parameters:
The only notable difference here is the value create_premiere which is set to true. This undocumented parameter seems to be the reason uploads created the way described in official documentation fail to work properly.
Now I wonder if there is a way to fix these uploads without having to upload them again…