I had a chance to have a quick look. You don't say which fare you were interested in (both the cheapest economy fare and the cheapest business class fare seem to have the same stopover rule), but both of those fares (plus the cheapest WT+ fare) seem to have the same set of routings:-
Code:
1. LON-BA-SCL
2. LON-BA/IB-MAD-BA/IB-BOG/CCS/MIA/MVD-LA-SCL
3. LON-BA/IB-MAD-BA/IB-BUE-BA/IB/LA-SCL
4. LON-BA/IB-MAD-BA/IB-GYE/LIM/UIO-LA-SCL
5. LON-BA/IB-MAD-BA/IB-RIO-G3-SCL
6. LON-BA/IB-MAD-BA/IB-RIO/SAO-BA/IB/LA-SCL
7. LON-BA/IB-MAD-BA/IB-RIO/SAO-LA-SCL
8. LON-BA/IB-MAD-BA/IB-SCL
9. LON-BA/IB-SCL
10. LON-CUN-LA-SCL
11. LON-NYC/PUJ-LA-SCL
That may explain why you're not able to use this fare to route via the points you were trying, if the routing you were trying was not one of the permitted ones.