If you're referring to a "How Goes It" time/fuel check, (more commonly done on long haul international flights), there are a number of reasons for doing it.
Besides the already mentioned fuel leak possibility some others that I can think of are:
Enroute winds different than forecast and flight planned for
Altitudes, mach#, or routing different than planned
Actual gross weight or CG different than reflected on the weight and balance record
Airplane not properly trimmed
Engine and/or wing anti-ice required enroute
MEL/CDL drag penalties or APU operation required by MEL/QRH
Weather circumnavigation
Clearance limit issues (eg enroute holding at an FIR boundary)
Wrong drag coefficient entry in the FMC
Some planes/engines in the fleet just perform differently than others
Many others that I can't think of....but Ppruners will.
If I misunderstood your question, disregard all of the above.
