Hi Margot,
I copy your error image here for easier access:
This message is due to unequal dimensions (different number of vertices) between the surface file (surf/lh.pial or lh.white) and the corresponding Brodmann atlas (label/lh.BA.annot).
I don't think any recent of version of FreeSurfer would write non-matching surfaces and textures/labels, I wouldn't know how to interpret that. But if you find any evidence that something has changed between FS6 and this dev version, let me know and I will fix it in Brainstorm.
If it is not an expected change of behavior of FreeSurfer it could be: a manipulation error on your end, or a bug in this development version of FreeSurfer.
Is there any particular reason why you use this version instead of the stable FS6?