order of class should be same in both files (cls & gct), so in categorical label, the cls file should be in grouped format (according your first example)

take a look at this link : http://www.broadinstitute.org/cancer/software/genepattern/file-formats-guide

"The third line contains a class label for each sample. The class labels are sequential numbers beginning with zero. The first label used (0) is assigned to the first class named on the second line; the second unique label (1) is assigned to the second class named; and so on. (NOTE: While most GenePattern modules adhere to this rule of 0 as the first class, some modules (such as GSEA) do not. Check the documentation for the module you are using if you are unsure.) The number of class labels specified on this line should be the same as the number of samples specified in the first line. The number of unique class labels specified on this line should be the same as the number of classes specified in the first line. "