It's not clear what you mean - the operation of the program should be no different on the command line versus the GUI.  All that matters is what method you use for the omit map preparation.  The default "simple" method ("iterative" might be a better name for it) is apparently incompatible with a twin law.   The "refine" or "anneal" methods will work fine with a twin law, but are far slower even if you have a big cluster.  What exactly are you trying to run?

The lattice symmetry option is already enabled by default.  However, if you already have R-free flags defined, it will not generate a new set; for this, you need to use the reflection file editor (GUI->Reflection tools).  However, if you're at the stage of generating a composite omit map, this usually means that you've already done refinement and have R-free flags already - in which case calculating maps or performing further refinement with a different test set is a bad idea.  If you want to change test sets in the middle of the refinement process, you should first do some simulated annealing refinement to un-bias R-free.

-Nat