I cant help you with Republic Commando but Knights of the old Republic 2 I have backed up with no problems! The only difference tho is I never use Alcohol 120% for Securom games! I use CloneCD for all securom games and choose 'Protected Game CD' as the Datatype. I have never had a problem with Securom doing it this way. However I use Alcohol 120 for all other protected games.
Could it maybe be a bad batch of blank Discs? I have seen some people use a particular brand without problems but then sometimes they get a bad batch? Just a thought?
Edit: I can tell you Knights of the old Republic 2 uses the latest Securom protection! (5.03.13)