What the Bio-Kleen #5768 saponifier does is react with the outside layer of flux and soften it up. Literally turning it into a soap. You need a spray cleaner so that this soap layer will be washed away which then allows the Bio-Kleen to react with the next layer. Rinse that layer off, etc., etc. The problem with ultrasonic removal is that the outer layer is slightly dissolved and that is the end of the reaction. In the meantime the solder is being exposed to an alkaline condition. The exposed solder turns a dull gray as the surface shine is etched off by the caustic solution.
Source: Kester Solder