I used these values for measuring armloss:

• Transmissivitity of ITM = 1.384e-2 * (1 +/- 1e-2) 
• Transmissivitity of ETM = 13.7e-6 * (1 +/- 5e-2)
• Mode-Matching efficiency of XARM = 0.912 * (1 +/- 2e-2)
• Mode-Matching efficiency of YARM = 0.867 * (1 +/- 2e-2)
• modulation depth m1 (11MHz) = 0.179 * (1 +/- 2e-2)
• modulation depth m2 = 0.226 * (1 +/- 2e-2),

then the uncertainties reported by the individual measurements are on the order of 6 ppm (~6.2 for the XARM, ~6.3 for the YARM). This accounts for fluctuations of the data read from the scope and uncertainties in mode-matching and modulation depths in the EOM. I made histograms for the 20 datapoints taken for each arm: the standard deviation of the spread is over 6ppm. We end up with something like:

XARM: 123 +/- 50 ppm
YARM: 152+/- 50 ppm

This result has about 40% of uncertaintities in XARM and 33% in YARM (so big... ).

In the previous measurement, the fluctuation of each power was 0.1% and the fluctuation of P(Locked)/P(misaligned) was also 0.1%. Then the uncertainty was small. On the other hand in my measurement, the fluctuation of power is about 2% and the fluctuation of P(Locked)/P(misaligned) is 2%. That's why the uncertainty became big.

We want to measure tiny value of loss (~100ppm). So the fluctuation of P(Locked)/P(misaligned) must be smaller than 1.6%.

(Edit on 10/23)
I think the error is dominated by systematic error in scope. The data of beam power had only 3 degits. If P(Locked) and P(misaligned) have 2% error, then
.
You have to check the configuration of scope.