Magic-Flight testing has not noticed any 'break in' period with the unit itself. We suspect that observations to this effect are much more likely to be associated with the batteries. The discharge profile for the first 15 seconds of use immediately after a battery is charged is different than the discharge characteristics for most of the remainder of the battery cycle. This curve itself changes depending on the number of complete charge/discharge cycles the battery has passed through, particularly for the first few cycles. Given the intensive usage and battery cycling that the Box imposes on the battery, these effects are somewhat more pronounced than would be evident from testing that the battery manufacturer would know of.
As such, we tend to think that this effect is probably due to a combination of the following two factors: 1) Changes in the battery itself, and 2) Changes in the manner that the battery is used. In particular, new users are more likely to pull the battery off the charger and immediately use it, whereas later, there is probably allowed a 'cooling off' period from when the battery is charged and when it is first used.
This is not to say that there might be some effect with the unit itself that has not observed or is not yet known, only that we have not detected such effects.