There's a chinese proverb "
A man who has a watch knows what time it is. A man with two watches is never sure"
At around 30 feet (OK I'm going to use metric equivalent of around 10 meters) ambient pressure is 2 atm so a ppO2 difference of .06 is like 3 percent difference in O2 concentration.
Are both sensors in the same bag? depending on where in the loop extra gas is added could be a possible?
How old are the each of the cells and are they genuine or third party?
Look at this link
Oxygen Sensors - Diving Industry
You'll see that both the D02 and D06 would fit the oxygauge but one is 6mV and other only 5 - wrong sensor = upto 20% error
Sorry but I don't know what you're diving but it might be a good diagnostic to calculate expected ppO2 at a given depth - this will give a good idea if one is right and the other is low (or high) or if they are both a little off.
e.g. on an SCR at 10m (2atm) on 40% nitrox, a loop flush would give theoretical ppO2 of 0.8
Not a lot of experience with the VR3 but some dive computers I've had in the past did get inaccurate on depth if salt built up around the depth transducer - stick it in a jar of fresh water for a few days.
I think the VR3 turns off above 3m - I did a dive with a guy in the shallows for about 70 mins and his vr3 logged it as only 22 mins.