An unless the day was overcast, I would expect more trouble from removing the diffusers than from using them. The M2 adjusts its sensitivity to compensate for light level. No other unit does, that I am aware of, so difference in light level and removing diffusers should make more difference for them than for you.
If you turn the tripod around 180° and swap the start and stop plugs, does the error change to E0? If so, that's a faulty sensor. Might be stuck on minimum sensitivity or something like that. If it continues to be E1, then the computer module has the problem at the input. Could be a circuitry problem, but loose jack contacts or a bad solder joint there could do it, too. The velocity coming up so short on the .45 makes me suspicious of the computer module, but I can imagine sluggish sensor response being an issue.
Anything you put on a bullet can throw its accuracy off by introducing mass asymmetry that causes wobble due to its high rate of spin, but I would not expect Sharpie coloring to be heavy enough to do that.
Coloring a bullet helps eliminate reflections from the ground, should you have a problem with that. Light colored gravel or concrete can cause the problem of picking up reflections off copper. Putting down black plastic on the ground should prevent it. I've never had a problem with grass or dirt causing this.
Gunsite Orange Hat Family Member
CMP Certified GSM Master Instructor
NRA Certified Rifle Instructor
NRA Benefactor Member