Hi Daniel,
Pardon the delay, I missed the board email message that said there was a new post.
D1 is the USR2 LED. This toggles on or off whenever a sample packet is received. If it remains off or appears "brighter" it is because the computer has momentarily stopped sending data to the LaserShark.
Debugging this is going to be extremely difficult due to the number of components involved.
A first step would be to identify if what you THINK is being sent to the LaserShark is correct. Has anyone analyzed the output of the scanning algorithm to determine if it is correct? Furthermore if you repeat the same scan, are the artifacts in the exact same spots?