Could it be that some of the fuel which passes through the flow meter gets recirculated by the fuel metering unit at lower throttle settings? A flow meter may not take account of fuel density changes with altitude/temperature either.
This document has some info about ways to achieve fuel savings on B737 & 757:
mdh.diva-portal.org/smash/get/diva2:121168/FULLTEXT01
I worked at Smiths Industries on the B777 ultrasonic gauging system (FQIS), and recall that one of its claimed advantages over capacitance units was its increased accuracy. Nevertheless, it has yet to be adopted on any other type as far as I know.