Well we all know the scavenge pumps can cause a slight imbalance, but this is fuel fed from the center tank and not added.
It could be this aircraft has a check valve at the center tank pump that is not seating completely. This would allow fuel to be back fed into the center tank from the respective main tank, 1. causing 'mystery' fuel to appear in the center tank, and 2. leading to a (non-critical) imbalance.
I like the faulty crossfeed valve theory, MH152. It could cause the imbalance, due to differences in main tank pump pressures, but it wouldn't account for the visits to the center tank from the fuel fairy.