747deiseldude,
Basically - JetPlanner uses average wind and temp forecasts at the selected levels on the great circle route, taking into account the diversion route and ground speed.
You may be flying a recipricle route, but once the everything has been factored in you will most likely find that the figures differ (as you already have)
As I said, thats a very basic view of why its happening - but if you want a (very) in depth explaination, look in yout Jetplanner users manual under POD/POA Commands............