I'm sorry -- I mis-wrote -- the Alpha feature ONLY works with the '**' continuous color scale, and doesn't work with the discrete (2-20) color panes.
The "feature" of clusterize that you are seeing comes from the way this functionality is written -- the clusterization parameters and results are bound to the overlay dataset, not to the image viewer. So if you are trying to clusterize the same dataset twice at the same time, the two viewers will end up in a war to see who controls the overlay dataset -- and like all wars, there are casualties. Without extensive re-implementation, this behavior will not go away (in AFNI or in reality).
I have modified the source code to show the continuous colorscale with the colors fading to white horizontally across the scale, if Alpha is on. The saved colorscale image will have the same feature. To make it horizontal, I'm afraid you'll just have to flip it yourself.
The re-built binaries with this addition should be available tomorrow (Tues 16 Dec 2014) morning. Please note that is Beethoven's birthday. And Jane Austen's. And Arthur C Clarke's. Time for a marathon reading of
Persuasion and
The City and the Stars, while listening to the
4th and 9th Symphonies, as played by Schroeder.