Hello Francesca,
The message is a warning so the results can still be OK. However from the rest of your message it seems like there is a problem in that the regions are not showing up properly in SUMA. If that is the case, I will need a little more detail regarding how things are misaligned in SUMA. Also, you should consider going the GIFTI route, whereby you use FreeSurfer to write the annotation file in GIFTI format that you can read directly into SUMA.
cheers,
z