I dont think we ever SEE Fredo actually RUNNING again, but if you feel your life is at risk staying in a certain place, you are going to leave.
Lets use Apple's plan for a minute- Fredo,upon Anthony leaving the boat, knows he's going to die(which he did know )He then simply gets off the boat.He now knows his life is in danger and is going to try to leave the dangerous place(the compound)Mike wont let him.Now that he's in that situation, he constantly has to look over his shoulder.
I'm not saying a brilliant guy like Freddie came up with this all at once. He knew when Anthony left, but if he truely did not want to face death, he could have thought this through and ended the trip early, before Neri had the chance to kill him.