I haven't had any problems with my SCI Studio games running under FreeSCI. They all work for me--the first/latest template games, Demo Quest, DG, Al Pond, etc.
FreeSCI should display messages telling you exactly what's wrong. It's most likely an error in your script. Sierra SCI is less picky and can run scripts with errors more often. You can see on the FreeSCI web site a list of Sierra's games with script bugs which run fine in Sierra's SCI.