Dear Andrew,
 
it seems we have found what caused the problem:
 
In NBSrun.m, line 183 reads: 
[nbs.GLM.y,UI.matrices.ok,DIMS]=read_matrices([fileparts(UI.matrices.ui),filesep]);
 
So, it seems that the path excluding the filename is passed down to "read_matrices". This causes long delays or errors (especially if you have lots of other stuff stored in the directory).
 
We have replaced it with:
[nbs.GLM.y,UI.matrices.ok,DIMS]=read_matrices(UI.matrices.ui);
 
This way, the path including the filename is passed down, and it seems to work.
 
Does this make sense to you? We aren't sure we understand the purpose of line 183.
 
Thank you so much!
Christian