Geosynchronous satellites orbits are not perfect circles so their apparent position wanders north and south of the Equator and they drift east and west in an figure-eight pattern. The position at any instant is monitored by ground stations and the offset of transmitted and received signals is compensated for the Doppler a Effect. Inmarsat was able to refine their model by examining not just the exchange of timing signals with MH370 but also with aircraft flying different know courses, speeds and altitudes over the past few weeks.
Presumably there is also a relativity effect when measuring tiny differences in elapsed time at 22,000 miles above the earth compared to an aircraft flying 7 miles above the earth. I don’t know whether it is big enough to be relevant, but if they are taking into account these tiny variations in the satellite orbit, these must be very small calculations they are making.