Problem fixed in this commit:
https://github.com/brainstorm-tools/brainstorm3/commit/25732db0073a343411ea2c88bebb5686873e41f9
The background removal detection added recently was removed. Only the manual definition of the threshold was kept.
To recompute the histogram for the MRI and get a fixed "guessed background theshold" when generating the head surface, simply display the histogram (right-click on the MRI > Display > Histogram)