The 3dPAR2AFNI.pl script is a user contributed script that sometimes needs tweaking to make it work for your data, and I wouldn't expect the slice timing to be accurately read. We usually assign slice timing on input or from raw or DICOM data with Dimon or to3d. To assign slice timing later, the 3drefit command can be used. Alternatively, 3dTshift can be supplied a slice timing pattern, and that's what you should probably try for your data. That won't sort out all the questions, but most are explainable, but it will probably be easier if I PM you with some instructions for uploading data. I'll take a look and get back to you.