It does make sense if the flights are on different airlines or on different equipment. It's costly to pre-position equipment so if you have to fly a plane to a location anyway it makes the most sense to reduce your losses (by dropping per-seat fares) rather than holding the line on prices and flying with empty seats.
Repositioning is one of the reasons I can think of for it, that and the fact that you get more security scrutiny on a one-way ticket than a two-way ticket. But why security scrutiny would equate a price difference is beyond me. I mean you're right, usually return tickets are cheaper than two one-ways on any number of systems.
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