Can we assume all you are changing is the shutter mode, and that the same settings are producing acceptable single shots? Are you using M, A, S or P modes? I don't think a mode that calls for flash will make dark images, but will stall instead, but that may vary.
Are the images just darker than usual, or are they quite black? Are they even, or banded?
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Are the images just darker than usual, or are they quite black? Are they even, or banded?