Nozzle reducing flow as it comes close to finish layer
If you think it is a slicing problem, look at the G-code. You might want to arrange for the infill to be orthogonal to the axes, but it ought to be easy enough to calculate the ratio between printhead motion and the extruder. G-code is just text, and fairly easy to make sense of. The RepRap wiki has a good reference to the commands, and all you care about are X-Y movement, and E movement.

An alternative explanation might be that your extruder is struggling with the extrusion rate, and after continuous extrusion is failing to heat the filament fast enough to melt. The layer change could be providing a sufficient respite that walls start off OK on the next layer. Also check (in the G-code) that the speed of walls and infill is the same.