I've had the same problem occur at times. The actual problem that multi-scan is designed to fix is digital "noise" occurring in the shadow areas. Noise is a random event, analogous to grain in film, so if you make several passes of an image and average them together, the averaging should eliminate the noise and give a cleaner image.
The way I understand the "blooming" you mention is pixel wells (sites) becoming saturated with too much signal and the excess electrons spilling over into the adjacent sites. It almost always occurs in sharp light to dark transitions. Multi-scan might fix it sometimes, but I know of no reliable way to completely eliminate it except possibly reduce overall exposure. I usually turn the slide around and scan it in the other direction. Sometimes that will reverse the light-dark transition and stop the "blooming".