Dear Haeme Park,
this looks very strange. You said that the preprocessed images look fine - did you visually check them with a reference to an image aligned to MNI standard space (like SPMs single_subject_T1.nii)? You should look at the images resulting from the last step of preprocessing that enter analysis (smoothed, normalised, realigned ...). To me, it looks as if SPM got slicing, orientation or positioning of your images wrong.
Best
Volkmar
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