A pickup adjustment should fix this easily. On most guitars the pickup dosen't sit exactly level, the high E side is usualy a little clocer to the strings than the low E side. Depending on the rest of your set up, the difference may be very slight or it can be very pronounced. Single coil pickups often require more of a difference than humbuckers. Very light guage strings will contribute to a loss of volume on the high strings too. The smaller the string, the less of a vibration field for the pickup to detect. You will most likely be better off to lower the low E side rather than raise the high E side.
