Algorithm difference in connectomestats NBS

Hello.

I am currently conducting a structural brain network analysis on my diffusion MRI data, using the connectomestats NBS algorithm. However, although the data (the connectivity matrices, design matrix, contrast and the threshold) itself was kept identical, while we were unable to find any significant subnetworks through the Matlab-based NBS GUI, when we ran NBS through connectomestats, we were able to find both positive and negative subnetworks at the same given threshold. I was wondering why this may be the case, and if the two algorithms are greatly different.

Thank you and have a lovely day!