When you discharge them the voltage drops due to the amp draw. When you charge them it does the opposite. You've all seen the Eagle Tree graphs, right? When the battery has a large load the voltage is lower than with a smaller load. Same with charging only the voltage goes up (duh). So, what Cpt. Obvious is trying to say is that a higher charge rate will cause the battery to hit the peak voltage sooner than it really should and so it starts to trickle before it has a chance to take in more mAH. Slower charging is technically more efficient because the battery reaches the same voltage but absorbs more of the charge that was put into it.
EDIT: If you are balance-charging don't pay any attention to what I said!
When you balance-charge at a slower rate, most of the extra mAH the charger says it put in comes from the extra charge that was "balanced out" over the longer period of time.