Freeview does not update in the viewer window to the correct slice position when calling on viewport. This means instead of taking snapshots of N slices of the brain from N specified slice coordinates, it takes the same snapshot over and over again.
Originally, we found a workaround by disabling qt_setup in the freeview tcsh script:
#source $FREESURFER_HOME/bin/qt_setup. 
After this, it worked perfectly. Since then, it has stopped working well. 

The error occurs for saggital and coronal views. (Axial works fine, for some reason). I am using the stable release of freesurfer 6.0.0. The problem still happens if I interleave axial/coronal/saggital viewport commands, instead of running them together as below. The problem also occurs using the development version of freesurfer from august 27th, CentOS7 build (but only for sagittal and coronal; Axial works fine).

freeview -cmd minimalcmd.txt

minimalcmd.txt:

freeview -v SUBDIR/mri/orig/001.mgz -layout 1 -cc -nocursor


-viewport sagittal -slice 80 127 127 -ss  OUTDIR/T1_sag_1.jpg -noquit 

-viewport sagittal -slice 90 127 127 -ss  OUTDIR/T1_sag_2.jpg -noquit 


-viewport axial -slice 127 80 127 -ss  OUTDIR/T1_ax_1.jpg -noquit 

-viewport axial -slice 127 90 127 -ss  OUTDIR/T1_ax_2.jpg -noquit 


-viewport coronal -slice 127 127 80 -ss  OUTDIR/T1_cor_1.jpg -noquit 

-viewport coronal -slice 127 127 90 -ss  OUTDIR/T1_cor_2.jpg -noquit 


-quit


In case it's useful:

uname -a

Linux ncfservice02 3.10.0-693.21.1.el7.x86_64 #1 SMP Wed Mar 7 19:03:37 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux


I'm unsure what else I can try or what other information I can provide. Please let me know.