Hi again,
You are right, the CSF segmentation is obtained from the FS image. In the meantime, I found a similar problem for one of my participants and was trying to debug.
It looks like the issue lies at the step of creating the CSF compartment from the FS labels, and I could see that the 5th ventricle image was not created correctly for this participant which then threw everything off.
You might need to check which of the images contributing to the CSF compartment are problematic, and you could potentially leave it out if it has a small coverage.
Nick