I made a bubble shooter capx a while ago. It also found connected bubbles with a flood fill algorithm. It only did it when a bubble landed as there is no reason to do it continuously. I also thought the lag to not be a problem because of when it occurs.
Some ideas to make it faster:
1. Lookup the capx I made and see if my implementation of flood fill is more efficient than yours.
2. You could limit the amount of lag by doing the flood fill over multiple frames.
3. As a last resort you could come up with some type of data structure to make the flood fill more efficient by making the picking of a bubble's neighbors a simple lookup instead of a collision check against all the other bubbles. In theory it will be much faster, but it will require a lot of events and be very tedious to setup.