Arduino flash trigger using laser and photodiode
Well it sounds like enough energy from your laser is going straight through the bubbles and hitting your photodiode. 

Try to ramp down the power on the laser, or put it through some sort of darkening filter such that it barely doesn't trigger when there's nothing in the way. Once that is sorted out, we can look at the timing problem. I suspect it has more to do with too much energy from the laser than anything else.