I grab 2 hours of the PD measurements using dlData_simple.ipynb in the misaligned state.
I get pretty much a normally distributed reading without drifts (Attachements 1 and 2).
The error in the reading is ~ 0.5%.
I am pretty sure this amount of noise is enough to explain the big noise in the Loss figure measurement.
The reason is that the loss formula is #(1-P_Locked/P_Misaligned+T1)-T2) where T1 and T2 are the transmissions of the ITM and ETM.
The average of the ratio P_Locked/P_Misaligned is ~ 1.01 for a loss figure of ~ 100ppm.
The standard deviation of the ratio is ~ 1% which is also the standard deviation of the expression in the brackets.
The average of this experssion however is ~ 0.01.
The reduction of the mean amplifies the error in the loss measurments by a factor of a few 10s!