I'm hearing that the new flight planning system (constellation) takes quite a bit of time to run each version of the plan.
Pure and utter uncorroborated scuttlebutt (this is a rumour network) is the flight planners don't have good visibility into the "internals" of the plan in progress to see where it is trending to add manual tweaks. Basically it spits out a complete plan. If the plan isn't suitable for whatever reason (read reduced payload), the planners have to completely re-run the plan (about 30 min) with the tweaks to see what pops out. Wash rinse and repeat.