There is no reason why it'd have anything to do with fuel flow - things are very different with jet engines. Besides which, remember that a lot of things that happen in the real world simply remain omitted in the sim.
I'd check your key assignment for shutting off the engines and ensure you aren't hitting this key by mistake...
My best guess is that you still have the autothrottle (A/T) engaged after disengaging the main AP....therefore, when you try and move the thrust levers, you'll remain with the power the AP decides necessary to maintain the figure on the MCP.
Next time it happens, take a screenshot of the panel.