QS contains (hard-coded) the primitive symmetry operators corresponding to all 230 space groups as given in the International Tables. For those space groups for which the Tables give more than one (alternative) settings, only one is supported by the program. I have tried to stick to the most common ones (eg C2 instead of B2, hexagonal instead of rhombohedral axes, etc), but this doesn't mean that you should re-index your data ignoring the good reasons that made you chose a different setting. Instead, you can keep your favorite setting and define the corresponding symmetry operators explicitly using the SYMMetry keyword as described on page (do not forget to remove the GROUP keyword from your new input file). Note that you can safely ignore all operators arising from the presence of a non-primitive lattice. Please also note that QS will not make any tests on the input matrices (not even a determinant calculation), so you have to type them carefully.