Indeed, the tPAC code was clearly not designed to handle scouts correctly.
I fixed this, so that the results from the 3 orientations are averaged, similarly to what is done in bst_timefreq.m. Please update Brainstorm and try again.
https://github.com/brainstorm-tools/brainstorm3/commit/fbf01f3ca6955d134ea5cbd21e09c1cc53573ffb
Note that in the tPAC process, the various vertices within a scout are never averaged together.
I'm not sure this is the expected behavior...
@Samiee @Sylvain Can you please comment on that?