Hm, I don't know why that could be, that is the string we look for in the code (inside get_slice_timing.m, line 8 parses like if strcmp(slice_mode,'alt-asc')). Are you setting the slice timing using:
export PESTICA_SLICE_TIMING="alt-asc"

Can you copy and send me the matlab line that is echoed to the screen when apply_PESTICA2 is run?  For example, I get:

matlab -nodesktop -nosplash <<<"addpath /mnt/netScratch/ebeall/pestica_afni_v2;[card,resp]=apply_PESTICA2(15,'S40vol+orig','S40vol.brain+orig','alt-asc'); fp=fopen('card_rawest.dat','w'); fprintf(fp,'%g\n',card); fclose(fp); fp=fopen('resp_rawest.dat','w'); fprintf(fp,'%g\n',resp); fclose(fp); exit"

My first guess would be environment problem, but there are other possibilities.
Erik