I would do it with SoX (Sound eXchange) and ffmpeg (or avconv instead of ffmpeg). SoX is "the Swiss Army knife of audio manipulation", an effects and audio manupilation & generation tool for the command line.
sudo apt-get install sox ffmpeg
Convert your ac3 file to a wave file. Since SoX cannot read ac3 files directly, this step is unfortunately required:
ffmpeg -i sound.ac3 sound.wav
Use SoX with the pad switch to insert silence at the beginning:
sox sound.wav sound.flac pad 0.150
This inserts 150ms of silence at the beginning of the audio file.
Look at the SoX Manual for more infos.
You can also do this in a single line, without the need for creating an intermediate wav file, by using a pipe:
ffmpeg -i sound.ac3 -f wav - | sox - sound.flac pad 0.150