did you check via "Review Design" whether the data is assigned correctly to your design? You should have a look at "Files&Factors" and check whether the files for each subject are picked up by SPM in the correct order. Issues might arise if you specify lists of files outside the batch GUI. In such a case, you would have to make sure that your file lists are column cellstr arrays. If the are row cellstr's, they will be assigned to your cells in a wrong way.