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Having wanted to fly SYD/PER/SIN and return, I found that it is cheaper to take up two bookings rather than take up one booking - that is, one SYD/PER/SYD and PER/SIN/PER...and you save on that very poor excuse of a 10,000 point stop over penalty.
Agree with Jezz, sometimes that is the easiest way. Similar to booking on-line, when if you research both one way and return flights (I'll use the Qantas web site as the example), often I have got two one way tickets for cheaper than the return selection that is offered. Also, with each internet booking getting you 1,000 extra FF points (if you don't need the flexibility of being able to make changes), it helps accumulate those FF points.