Basically, your charger is reading voltage under load - you are pushing current in to the battery, against the internal resistance. That will no doubt lead to heat being generated, which will alter the internal resistance. As the voltage and current changes during the charging process, the temperature will change, and hence the resistance will change, and so on.
What I'm getting at, is that during the charging process, things are changing constantly. No surprise then, that once the battery is removed from that process, you are looking at an entirely different set of circumstances again, and if you measure the voltage with a DMM, you are now seeing a different value - the voltage when the battery isn't under a load. It isn't unusual for this value to be lower than the CV voltage that the charger is set to.
Basically, voltage under load and voltage with that load removed are going to be different.
As okwchin stated, how big a difference there is between the two values can be related to cell condition. V=IR, so the higher the internal resistance, the higher the voltage will read for a given current. Likewise, the higher the charge current, the higher the heat generation, which could also have an effect.
So long story short, your charger is charging to 4.2v, as you can see in your charts, but that voltage is being measured under load, and that load will have an effect on the voltage being measured. Remove that load - remove the battery from the charger in other words - and the conditions change, which in turn leads to a different voltage being measured. A lower resistance cell, or a lower charge rate, would most likely lead to there being a smaller difference between the voltage under load and the voltage off the charger.