To follow up, SPM will support uncompressed 4D files, it appears that your data was compressed. You will have to select all of the frames. This is done by typing 'inf' in the frame selection box, which is located just beneath the file filter in the SPM file selector GUI. Alternatively, this can be done by using the batch module "Expand Image Frames"
Additionally, some sequences do not discard dummy scans by default, even on SIEMENS scanners. If you wanted to mimic default behavior, use the following:
Dummy scans = ROUNDUP(3001/TR)
which is typical SIEMENS behavior. Thus, for your 400ms TR, you could discard 8 volumes.
The MRIQC data driven approach could suggest the removal of more volumes - sometimes the default is not sufficient.