FAQ

The generated SWF file was locked, when I tried to import it into my FLA file.
Due to the optimization of the SWF generating engine, all the contents will be flattened when you try to import it into MacroMedia Flash. If you want to reuse the generated SWF file, please create an empty Movie Clip and use its loadMovie method.

What is the difference between PowerPoint to Flash and the command line version?
The difference is the license type. The desktop version was designed to be installed on PC for personal usage. It has a friendly user interface. While the command line version was designed to be installed on server side for automation. Technically, they use the same converting engine.