Hi Andrés,
StarAlignment also shows an error dialog that the user has to close. This is a problem when using it in a script. It would be very interesting if there would be a parameter to configure this behavior.
This is now fixed. StarAlignment has a new 'noGUIMessages' Boolean parameter. If you set it to true before running the instance, no GUI message boxes are shown. In this case all output, including error information, is sent only to the console.
When the process can not find a solution the script is stopped.
This should not happen. I am working (with Vicent) to identify and fix the cause of this problem.
All the fixes will be available in RC4 (a matter of a few days).