But just a thought I had, but I am no expert at all in permutation tests as I am still discovering them: I think it might not necessarily be a bug but an inherent feature of the permutation test at the group level with very skewed groups: since we only have one subject in GROUP_A, any other permutation is just (GROUP_B - 1 GROUP_B's subject + 1 GROUP_A's patient), so I guess the variability will be in fact close to none and the result of the permutations always be very close to GROUP_B. So when we do a contrast, the correct labelling will be super significant compared to all other permutations of the labels, since all permutations will basically be the GROUP_B average connectivity.

If this reasoning is correct, this means that it is useless to do a permutation test with only a single subject in one group, because anyway the controls group will always ensure a stable null hypothesis based on only the controls, thus it will always make any voxel significant in the single subject when we do a contrast... I don't know if this makes sense :-/