I've noticed this happening on about one out of three flights over the last decade. It has improved since the early days with software mods but you still expect some discrepancies - it's even got a name now: "mid-Atlantic dip"!
The good thing is that the accuracy returns as the amount reduces, so the danger of running dry unexpectedly is small.
I remember being over the middle of Khazakstan about 10 years ago, looking at the scenery, when the "fuel imbalance" checklist pops up... OK, 2T difference, let's see what's in the tanks... Oh, the total seems to be going down by at least several tonnes a minute - that's not good - might have to shut one down. Got the 3rd pilot to go back and see if there was any indication of a fuel leak: no. Were just contemplating chopping the motor on the offending side when we noticed that the "leak" had stopped and we seemed to getting a bit of in-flight refuelling.
As the indicated imbalance was in the order of 15T, we took the autopilot out and let go: steady as a rock. Hmmm. Over the next 20mins or so the fuel displays returned to normal. We also checked the expanded engineering page which shows the fuel at each of the measuring stations - this was very uneven and depicted somewhat of a 'slope' on something liquid, which was rather unlikely. We were told later it was a software issue with failed sensors messing up the readings, rather than being excluded from the calculation...