I was not able to reproduce this issue with 1/f data only and the current version of Brainstorm. However Luc's figure looks very similar to the previous normalization issue that was fixed with Psd and fft amplitude normalization / scaling / units fix by Moo-Marc · Pull Request #346 · brainstorm-tools/brainstorm3 · GitHub, which would have given a factor of 2 difference.
@Luc, can you double-check that you have the latest Brainstorm and that you're using the 'physical' normalization everywhere? Can you also confirm that the figure above was not using the exact same data for the 2 different windows? I think you mentioned your peaks were taking into account the power of the aperiodic, so that might explain why the peaks look ok.