Changes in brainstorm functions that doesn't work when scripting

Hello,

I have another question regarding the same matter. I generated this script with Brainstorm interface:


And when I run it these messages appear in Matlab:

But when I did the exact same steps but with the interface it's not the same messages that appear, and it has consequences on the SNR and a small difference with the localization computed. I don't understand why it doesn't use the diagonal components from the noise covariance matrix. When I launch the same thing from Brainstorm I have these messages:

Is there an option that I have to change to obtain the same results with both the interface and the script?