Permutation t-test'ed Coherence NxN Fc graph

Hello!
The latest update solved our big problem with the two subjects that didn't display at all, thank you!
Still some "positive"-value (yellow-coloured) links appear in the Functional Connectivity map when we move the Intensity Treshold -slider inside the negative area of the parameter.
Does it has something to do with the Magnitude-square -option that we have used in these matrices?
Or is this possibly because of Coherence NxN with magnitude-square option gives always only positive connectivity values, as its "^2"?
If so, what kind of tool would possibly give negative values("blue lines") to Functional Connectivity graph?
T & H