It is probably a bug of the encoder. I don't think it has been tested with such small files. The workaround is, as you have already noticed, to leave some silence at the end of the sound.
Anyway, I would advise you to export the sounds at full quality, and encode them later using another encoder like "Lame" for example, which is free:
It's good to have a copy of the sounds at full quality, you never know when you will need them again!