Hi dream747,
We had exactly what you described about 10 years ago.
Once we had almost 200 kgs of centre tank fuel which we could not use (due pump low pressure lights on when the pumps were running.) The fix was to put about 500 kgs of fuel into the centre tank. The higher fuel quantity then enabled the pumps to prime and we were able to use all the fuel on the next sector.
Airbus produced a document (I'll try to find it) about "wet & dry sensors" in the centre tank & an "over run timing logic" to control the pumps. If the centre tank pump switches are left on during refuelling, the pumps receive a continuous "run" signal (even when the tank is dry). This will bring on the low pressure warnings (after a short time delay) and may cause the pumps to loose their self priming ability.
After refuelling and the centre tank pumps are turned on again, the timer circuit prevents the pumps from running dry before the low pressure warning is given.