This has nothing to do with whether your passwords are shadowed or not. It also has little to do with automation vs. doing it by hand.

The traditional crypt() function is 3DES. The current de facto standard is MD5. Some crypt functions do one, and some do the other.

GNU extension
On Linux in particular, and perhaps elsewhere too, the system crypt() call uses 3DES if the salt does not begin with "$1$" and MD5 if it does.

3DES takes a two-character salt. MD5 typically takes up to eight after the "$1$". Try using more salt characters if your salt is not long enough, and check to see if you must use "$1$" on your system as a prefix to the actual salt characters.

Christopher E. Stith
use coffee;