Why are different routes flown between the the same pair of airports?
Lots of reasons are possible, ranging from winds to other issues. In this case I'm willing to bet that the first flight was based on the most efficient routing to take advantage of tailwinds en route and that the second was avoiding Syrian and Turkish air space because of the political issues there earlier this year.

See also:


Flight Delays Incurred Avoiding Syrian Airspace
Royal Jordanian stops flying over Syrian airspace