Without the actual commands you ran, it is a little unclear where the problem is. The 3dZcutup command extracts only the slices you specify in your script. 3dZcat will only concatenate the partial datasets you specify too. There may be some problem with your script.

First you should be sure the original data was brought into AFNI as the number of slices you expect. If the raw data had been stored in DICOM, the data will usually be stored as single slice files - a single file for each slice. After converting the data to AFNI or NIFTI format possibly with to3d, 3dinfo will show the number of voxels in each dimension.

3dinfo dset+orig

The number of voxels in the Z dimension corresponds to the number of slices. The number of slices (z dimension) can be changed by programs that resample the volume to have different numbers of voxel or change the orientation so that 'z' does not mean the same thing. 3dresample is one of these programs. In any case, these are just guesses without some more information. Also note each dataset contains a history of the commands that have been used to create it, and that history is also visible with the 3dinfo command.