I have two identical Red Hat 6 boxes, to run recon-all-s. 

I just realized that in one of those I had freesurfer 5.3 for CentOS4 and in the other one I had freesurfer 5.3 for CentOS6. 

I have one experiment were subjects used boxes indistinctly. 

According to how the software is built, should I expect different results among them?

Many thanks for your help,

Gari