The bike's fuel consumption display is hardly a precision instrument, but most of us find that it correlates fairly closely to hand-computed averages. Mine is slightly optimistic - about 3-4% - which seems to be commonplace on these things, for both bikes and cars. ("Optimistic" means it reads a higher number on a miles per gallon basis, or a lower number on a liter per 100KM basis.)
As others are alluding to, you really have to do some averaging over a few tanks to be able to make a statistically-valid comparison. For example, on any individual refueling, you might under or overfill the tank by a half-liter or more, which dramatically alters the hand-computed mileage for that tank. The only way to damp out these variations is to get some long-term averages.
If you've got good data to show the numbers drifting apart, I would think the next question is whether the bike is actually getting worse mileage or it is just an instrument problem.
- Mark