I was sitting around for a couple of hours waiting for a bunch of files to convert.
Is it possible to invoke Remaster from a script ?

This way I could invoke Remaster from an Applescript or Automator and leave it running at night. And set it up to shut down after its done.

i not use it under mac, but under pc if you go in the cineform folder, you can find many command line tool to convert, mux, demux, correct cineform movie. try to check cineform folder, under tools.
i know that cineform dev team is different from pc to mac, and reason that force me to move from mac to pc is that some tools are not avaible (at this time) in the same way under mac OS.