Hello again,

Problem has been solved. Turns out the datatype not that relevant after all.

If you experience this problem with the 64bit mricron: Unselect the option "View" -> "3D Smooth Overlays" and restart the program.
(alternatively: In the mricron.ini file (hidden on windows systems e.g. in Users//AppData/Roaming ) the option OverlaySmooth has to be set to 0.)

On why recreating the nii with SPM helped me before, I am still clueless.

Thanks to Chris for the quick reply and the support!