My software is generating this warning because I have never seen an image like this before, so you should excercise caution when processing the data. As you note, the image is correctly identified as 'alternating decreasing' slice order. However, Siemens images are typically stored to disk as a mosaic with the upper left being the most inferior slice and the lower right being the most superior, regradless of the order of acquisition. In this case, my software is not sure if this is correct, or if the upper left has the most superior slice. You will want to confirm the order of how slices are saved to disk, particularly if you want to perform slice time correction. If you want, you could send me a DICOM directly to my email address for me to validate. Otherwise, you will want to pay careful attention to this page
  http://www.mccauslandcenter.sc.edu/crnl/tools/stc

To quote the critical section of SPM12's slice timing help:
  Note that slice ordering is assumed to be from foot to head. If it is not, enter instead: TR - INTRASCAN_TIME - SLICE_TIMING_VECTOR'

In your case, I am not sure of the slice ordering of the raw data, as I have never seen this sitatuon.