We've used ALSCRIPT on Sun Workstations and Silicon Graphics for some time, with very large alignments and command files with thousands of commands. All seems to work OK, the program has not crashed on us at all!!
However, the command interpreter in ALSCRIPT is very simple and the program will crash if you give any command the wrong number of arguments (e.g. leaving out the shade value in a shade_charscommand).
Also, the program will crash if you give it out of range sequence numbers. e.g. refer to sequence 38 when there are only 20 sequences in the block file.
I hope to include error checking for both these problems in a later release of the program.
If you do make the program crash, have checked all the documentation and your numbers, and the program still crashes. Then send me the command file and block file that causes the crash and I will try to investigate.
Suggestions for improvements to the program are always welcome.