Indeed, I could reproduce this behavior, with only one file, and 2 or 3 scouts, independently from any other options in the process. The function PhaseTE_MF behaves differently for 2 or 3 signals.
Examples at line 577 in bst_connectivity:
[dPTE, PTE] = PhaseTE_MF(permute(DataAband, [2 1]));
Two examples for DataAband (for the second figure, the 3rd signal was removed):
PTE1 =
0 0.2320 0.1752
0.1587 0 0.1992
0.5978 0.5174 0
PTE2 =
0 0.1394
0.2450 0
@MartinC @hossein27en @Marc.Lalancette @Sylvain
Is this expected?