Done the same work in a C404 as well as pax transport. Lovely machine. Sounds as though your aircraft is fitted with the same pumps as the ones I have flown.
Only suggestion I can make is to turn the pumps on low when next you see the fluctuations. If the fuel flow continues to fluctuate then it is the gauge - if it stabilises then where does it stabilise?
It should be a higher reading than before the pumps were turned on. You will have noticed that when turning the pumps off after take-off the fuel flow reduces, quite substantially. However, it does sound like a gauge or a sensor unit that is operating intermittently.