I always balance charge, at the end of the day I charge the batteries back up to storage voltage independently, when I come to charge my batteries for a days flying they are all essentially at the same voltage, and so I parallel charge them. I connect the power leads first.
Colin, you'd have thought that voltage readings would be very similar from measuring device to measuring device, but like you I see variations. I guess it comes down to what you're prepared to pay for. If you look at electrical components they will state their accuracy, so a carbon composition resistor might have an accuracy of +/-5%, metal film resistors might be +/-0.1% one will be more expensive than the other. I only use the battery checker to check which is the full battery.