Dear Thomas,
in some designs, I remember SPM to reorder your list of images. You should not only check the covariate ordering, but also the order of images in the final design.
If you used a script to specify your design and don't find the images and covariates in correct order and correspondence, you may want to check that the image list for each subject is a column cellstr, not a row one. Similar, covariates should be column vectors, now row vectors.
Hope this helps,
Volkmar
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