I never knew what the difference was between LAN Peru/Ecuador. When I check in at LAX, it's always the LAN counter. Never had I seen LAN Peru. Plus, they all use LAN metal. The only difference is the flight code.
But in terms of getting miles credited, there is a difference. LA coded flights get credited much faster than LP coded flights. On two occasions, I had to send my boarding pass and receipt to AAdvantage to get the mileage credited from LP.