Dear Konstantinos,
my best guess is that the warped atlas maps have a slice ordering that differs from the slice ordering of your native T1. As long as the mm origin corresponds in all images and Check Registration shows good alignment, everything should be fine. As long as the "Images do not all have same orientation and voxel size" is only a warning or you are using spm_imcalc, spm_slice_vol or spm_sample_vol to read the data from specified mm coordinates, you can safely proceed using the data without explicit reslicing. You would only need to reslice if you really need a 1:1 correspondence of the voxel values saved on disk.
Best,
Volkmar
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