It depends on what you mean by 'properly'
Talairach warping is not nearly perfect, particularly because brain anatomy is so variable.
So, if the centers are hideously off or there is clearly something wrong, then please describe the problem further.
However, if M1 looks like its overlaying on S1, then you have to grin and bear it.
A sophisticated but slightly cumbersome (sorry Ziad, not very cumbersome though) fix to accommodate intersubject anatomical variability is surface normalization. Look at FreeSurfer and SUMA.
-Prantik