Hello again,
Just another update: I tried running Lee Sigma instead of Gamma Map to check if I could reproduce the errors I was getting. I found that there is no difference between Lee Sigma manually done and when it is run through the code. Both the images are filtered correctly. I did this for both S1 and R2 images. Could this be an issue with the way the Gamma Map SF is set up in snappy?
Thanks for your time.