For distribution reasons, the FFT algorithm has been changed in SPro 3.3. Some minor changes have also been made in the code. Those changes result in slightly different features between SPro 3.3 and greater and the previous versions. Those differences are minor but it may slightly change the results in any automatic recognition system trained with some features computed from previous versions of SPro.
Some option switches have also changed so that the same letters mean the same thing accross all tools. Please pay attention to your old scripts when upgrading to the current version. However, long option names have not been changed so it may be a good idea in the future considering to use the long option names...