Is it recharging properly, and still giving several hours of playing time? Unless you experience an actual problem with recharging and playing time I wouldn't worry too much about the light indicators.
There may not be an actual problem here. The light indicators may not be a perfectly linear representation of charge remaining. In other words, the length of time the indicator remains in the 2-light position may simply be shorter than the time it shows the 3-light or 1-light position. And since the battery still drains some even when there is no cord, the overnight drainage may simply have moved through the 2-light position normally.