The program IS doing the Winsor filter for each sub-brick -- it just was printing out the message for only the first sub-brick.
I've patched the program so that its messages are more consistent. Also, I added a "-verb" option to have it print more verbose progress messages, which will let you see what it is doing and in what order. However, these changes won't be compiled or distributed until the major change to AFNI that I mentioned is stabilized.
Please note that the order of the options on the command line does NOT affect the order of the operations as they are carried out.
bob cox