Weird, I literally have not had LapTracker miss a lap in tens and tens of thousands of laps. I have my phone in a cheap tripod I bought off Amazon looking down at about a 75* angle. I am not sure if this is helpful at all but here are some screen shots of my set up.
Thanks for the reply. My settings are pretty much the same. I'm still not sure what the problem is. I'm going to turn on some lights, maybe it needs more light.