Hi Darren,
In general the two commands you have should produce exactly the same thing. Your code in the previous post looks fine. One thought I had is that when you start up AFNI to look at these datasets, the threshold slider bar is in the middle of the range. This may clip values (that exist) in the -1clust dataset, but not in the -1clust_order dataset. This is because the -1clust_order has integer values, while the -1clust has, possibly, fractional values. Make sure the slider is pulled to zero.
Just a suggestion,
-jim