Yes. This is the same issue that has existed with OnAir Company since the plane rolled. I remember someone saying before it's not writable, and I too looked at the ref list and noted it's not directly writable. I'm not sure how it gets set as I don't develop addons for x-plane but clearly something that is done ends up affecting this dataref as the pump is affecting it.
I realize this is maybe a trivial issue for you guys to chase as it affects a very small number of your customers, so I did some digging around datarefs (in game) to see if I could find any odd settings as I turned the pump on and off in order to see if I could uncover any sort of correlation, but obviously without being able to see the code it is pretty difficult to know what to look for and keep track of the dozens of ref's. that said, I did find a few things I felt were odd, Perhaps they are not, as I said I don't develop for x-plane but I'll point it out and you guys can decide. sim/cockpit/warnings/annunciators/ and sim/cockpit2/warnings/annunciators/
fuel_pressure
fuel_pressure_low
These are set to 1/true any time the pump is off. No matter how much throttle you apply. To me it seems these should shut off as pressure is increased through power, but they don't seem to update other than by the fuel pump switch. Not that this would directly affect the other ref.
/sim/flightmodel2/engines/
engine_has_fuel_flow_after_mixture
engine_has_fuel_flow_before_mixture
These two remain 0 unless the fuel pump is on. I noted that has_fuel_flow_before_mixture is writable if override_fuel_system is true. I tried setting override_fuel_system to 1 in the editor; it took but still would not allow me to adjust has_fuel_flow_before_mixture so couldn't test results.
/sim/cockpit2/engine/indicators/
fuel_pressure_psi
While this is once again is a read only ref, I find it odd that this shows 0 unless the pump is on. I'd think if the engine is running it'd have fuel pressure.
/sim/flightmodel/engine/
ENGN_running
This one has me mildly excited. This ref is writable per the documentation, but I can't get it take a change in the ref editor. However, it shows 0 when the fuel pump is off, and changes to 1 when the fuel pump is on. This ref seemed to me to have the best chance of being tied to the engine_is_burning_fuel in some way. With the pump on, this ref point behaves as I'd expect it to when turning the engine on and off. But as soon as the fuel pump is off, it no longer behaves as I'd expect.