A half-century-old border dispute between Peru and Ecuador has flared into military skirmishes. Peru said today that Ecuador had downed one of its army helicopters, killing all five crewmen aboard. Ecuador, meanwhile, ordered state employees to turn over two days of wages so that its forces would have "adequate funds to allow it to confront the current emergency." At stake is a 50-mile stretch of mineral-rich jungle. Pope John Paul II joined South American leaders in appeals for a peaceful settlement of the conflict, which began with minor clashes three weeks ago. Tomorrow, Peru and Ecuador are scheduled to attend the long-scheduled international meeting of the Rio Protocol group, which set the disputed border 53 years ago.