When I run the program, I get the output below. (The line starting with % is the command line I used.) If you aren't seeing something like this, then perhaps your AFNI binaries need updating.
% 3dAllineate -base SSanat0101+orig -source SSanat0102+orig -allcostX
++ 3dAllineate: AFNI version=AFNI_2008_07_18_1710 (Nov 10 2008) [32-bit]
++ Authored by: Emperor Zhark
++ Loading datasets
++ Zero-pad: not needed
++ Computing -autobox
++ 3597048 voxels [44.3%] in weight mask
++ Number of points for matching = 1690612
++ Local correlation: blok type = 'RHDD(6.54321)'
*+ WARNING: No output dataset will be calculated
++ ========== sub-brick #0 ==========
+ initial Parameters = 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000
++ allcost output: init #0
ls = 0.301248
sp = 0.300433
mi = -0.387601
crM = 0.277303
nmi = 0.938519
je = 5.91662
hel = -0.0747492
crA = 0.526601
crU = 0.528975
lss = 0.698752
lpc = 0.0262987
lpa = 0.973701
++ total CPU time = 6.8 sec
++ ###########################################################
