In my experience, LAN messes up sometimes with LanPass Kilometers, back when O fares were up for sale for Joung Chilean Students (somewhere between 2004-2006, and a 50% off the cheapest price), even when fare said no LANPass accrual, 75% of the time I got the kms. anyway, this between CCP and SCL. Now they don't sell those anymore, but new fares really stand close to those O fares.
In my last paid trip with LAN, also btw CCP and SCL, flying in "Base" fares, but different booking classes on each leg, I got 25% kms for the first leg, and 100% kms. in the second leg, and though it was a higher class, it was still "Base" and got 100% kms, and got the qualificating legs for both flights.

Not going to strive for more this year, though, I'm a premium because of the credit card from the bank, so going to Silver would require a lot more time, and college is really giving me a hard time now.