Hi Maddy, 

I did a run and I noticed there are difference between the two versions. Nevertheless, the output for the run I made looks acceptable. 

The problem with version 1.4.1 was that during the execution, some of the parameters were not passed correctly to other scripts and it was not possible to execute it sequentially for multiple cases. Most of the changes were done to allow consistent execution when running it this way. 

What atlases are you using for the skull stripping? Are you using the same ones for both runs? 
Are you using T1 and T2 images?