That sounds weird, I would have thought that using a double boiler type set up like you describe would be fine for evaporating. As you say, the temp is never going to exceed 100 degrees C, and if the alkaloids in acidic solution can handle being boiled, it seems to follow they should handle evaporation at a similar temperature just fine.
Were you using the same batch of Mimosa each time? Or did you do something else different between trials, like packing it into gelcaps this time but not the last time?