Dunno if this is causing your difficulty, but one difference is the PATH (and other environment variables) in the two cases. In "do shell script" you get a totally stupid PATH set for you (including your HOME directory of all things), while in your terminal version the PATH is rather more standard.
Insert an "echo $PATH" into the two commands and have a look at the result in each. Could be that your flic.command is making some assumption about the PATH that is failing somehow. Try using absolute paths inside flic.command and see if that helps.
Cheers,
Paul