The size of the bubbles has more to do with surface tension than how active the fermentation is. I brewed a Scottish ale a few days ago, and the first day it had the appearance of a Yellowstone mud pot. The krausen was very dark and thick with very large bubbles. By the end of that day the krausen was lighter in color and the bubbles were smaller, although fermentation was more active. Something in that dark material was very strong and allowed large bubbles to form before bursting. I don't know why there would still be krausen and bubbles in secondary, though. Need more information on yeast and grain bill.