I thought Bill Clinton pardoned the members of FALN. How did Morales not receive his?
Probably because he was not in prison here. From Wickipedia:
On August 11, 1999, Clinton commuted the sentences of 16 members of FALN, which is a Puerto Rican paramilitary organization that set off 120 bombs in the United States, mostly in New York City and Chicago.
So Clinton commuted their sentences, he did not pardon them.